protein domains :: essays research papers

Describe the Nature, Structure, and Function of Domains in Proteins Domains "Within a single subunit [polypeptide chain], contiguous portions of the polypeptide chain frequently fold into compact, local semi-independent units called domains." - Richardson, 1981 In the hierarchial organisation of proteins, domains are found at the highest level of tertiary structure. Since the term was first used by Wetlaufer (1973) a number of definitions exist reflecting author bias, however all of the definitions agree that domains are independently folding compact units. Domains are frequently coded by exons and therefore have specific functionality. Among the many descriptions of protein domains the two most striking and simple are " Protein evolutionary units" and "Basic currency of Proteins". Domains may be considered to be connected units, which are to varying extents independent in terms of their structure, function and folding behaviour. Each domain can be described by its fold. While some proteins consist of a single domain, others consist of several or many. A number of globular protein chains consist of two or three domains appearing as 'lobes'. In other cases the domains may be of very different nature- for example some proteins located in cell membranes have a globular intracellular or extracellular domain distinct from that which spans the membrane. Protein domains occur in large polypeptides, (proteins that have more than 200 residues). These proteins have two or more globular clusters which in turn have domains composed of 100-200 amino acids. Thus many domains are structurally independent units that have the characteristics of small globular proteins. If we examine the detailed structures of many transmembrane proteins, we see that they often have three different domains, two hydrophilic and one hydrophobic .(fig 1&2) A hydrophilic domain (consisting of hydrophilic amino acids) at the N-terminus pokes out in the extracellular medium, a hydrophobic domain in the middle of the amino acid chain, often only 20-30 amino acids long, is threaded through the plasma membrane, and a hydrophilic domain at the C-terminus protrudes into the cytoplasm. The transmembrane domain, because it is made of amino acids having hydrophobic side chains, exists comfortably in the hydrophobic inner layers of the plasma membrane. Because these transmembrane domains anchor many proteins in the lipid bilayer, these proteins are not free-floating and cannot be isolated and purified biochemically without first dissolving away the lipid bilayer with detergents. (Indeed, much of the washing we do in our lives is necessitated by the need to solubilize proteins that are embedded in lipid membranes using detergents!)