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Binding may refer to:

Joining physical objects together:

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Wikibooks

Up to date as of January 23, 2010
(Redirected to Structural Biochemistry/Binding article)

From Wikibooks, the open-content textbooks collection

< Structural Biochemistry

General Information

One of the functions of proteins is to bind different molecules together. A ligand is a molecule that is recognized by a protein and is able to bind to the target protein. The site at which the ligand binds to the protein is called the ligand-binding site. The ligand-binding site on the protein is quite flexible, making it easier for the ligand to bind to it. Ligand-binding sites are complementary to the protein to which it binds to. As expected, shape plays a significant role in fitting the ligand to the protein. In addition to that, the charge of the ligand and protein also plays a role.

Similar to the ligand-binding site, an active site is a cavity in the protein surface to which enzymes bind to. The active site is surrounded by amino acids that have the highest affinity to the enzyme that will carry out the reaction. Once again, the shape, charge and polarity of the amino acids affect the binding effects of the enzymes.

There are two models for how an enzymes fits into the active site: the lock-and-key model and the induced fit model. The lock-and key model assumes that the active site is a perfect fit for the enzyme. This model is a more rigid model that does not allow any modification of the active site or the enzyme. The induced fit model is a derivation of the lock-and-key model which still assumes that an active site is designed specifically for the recognition of one enzyme but both the active site and enzyme are flexible and can slightly modify to create the perfect fit.

In summary, the properties of proteins that affects the ability of enzymes to bind to it are its flexibility, complementarity, surfaces and non-covalent forces. The flexibility allows an easier fit between binding sites and enzymes. The complementarity and surfaces are important factors that contribute to the specificity of an enzyme to the binding site. It may be assumed that covalent forces are used due to their ability to better bind to the enzyme to its active site. However, the strong binding forces of covalent bonds makes it too difficult for active site to release the enzyme. It must be kept in mind that the enzymes do not bind forever in the active site and as a result non-covalent forces are the best for easy recognition of the substrate and releasing it.

PDB 1a40 EBI.jpg

Note: Above is a phosphate-binding protein

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