How Proteins Bind Other Molecules

Proteins can bind other protein molecules, DNA or RNA, polysaccharides, lipids, and a very large number of other small molecules and inorganic ions and can even bind dissolved gases such as oxygen, nitrogen, and nitric oxide. Binding sites are usually very specific for a particular ligand, although the degree of specificity can vary widely. Usually the binding is reversible so that there is an equilibrium between the free and bound ligand.

A binding site is usually a cleft or pocket in the surface of the protein molecule, which is made up of amino acid side chains appropriately positioned to make specific interactions with the ligand. All of the forces that stabilize tertiary structures of proteins are also used in ligand-protein interaction: Hydrogen bonds, electrostatic interactions, the hydrophobic effect, and van der Waals forces all have their roles. Even covalent bonds may be formed in a few cases—some enzymes form a transient covalent bond with the substrate as part of the mechanism used to effect the reaction.

Cell Biology: A Short Course, Second Edition, by Stephen R. Bolsover, Jeremy S. Hyams, Elizabeth A. Shephard, Hugh A. White, Claudia G. Wiedemann ISBN 0-471-26393-1 Copyright © 2004 by John Wiley & Sons, Inc.

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Figure 11.1. The glucose carrier switches easily between two shapes.

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