Structurally variable regions

A sequence alignment establishes the correspondences between the amino adds in th unknown protein and the template protein (or proteins) from wliich it will be built. Th three-dimensional structures of two or more related proteins are conveniently divided int structurally conserved regions (SCRs) and structurally variable regions (SVRs). Ihe structural conserved regions correspond to those stretches of maximum sequence identity or sequenc... 

List of Abbreviations GPCRs, G-protein coupled receptors PDB, protein database SCRs, structurally conserved regions SVRs, structurally variable regions... 

Deane, C.M. and Blundell, T.L. (2001) CODA a combined algorithm for predicting the structurally variable regions of protein models. Protein Sci. 10 599-612. 

The major challenge in comparative modeling is the treatment of structurally variable regions (SVRs). Especially flexible loop regions lacking a structural template are difficult to predict, since the calculation time increases nearly exponentially with the degrees of... 

Figure 1.10. Generalised structure of the variable and constant domains within antibodies. The variable regions (dark shading) of either the light or heavy chains are indicated as VL or VH, respectively. The light chains also possess one constant region (CL), whereas the heavy chains possess either three or four constant regions (Ch)-Ch4). depending upon the class of immunoglobulin (see text for details).

Figure 7.4 Basic structure of an IgG molecule. Two heavy chains (440 residues) and two light chains (214 residues) are joined by disulphide bonds and each shows a relatively constant amino acid sequence in one section (C-terminal end) and a variable sequence section (N-terminal end). The variable regions of both heavy and light chains are involved in the formation of the antigen-binding site.

The basic structure of an immunoglobulin molecule, such as the major serum antibody IgG, consists of four polypeptide chains two identical light chains (molecular weight around 25 000 daltons) and two identical heavy chains (with a molecular weight around 50 000 daltons), cross-linked by disulfide bonds to form Y-shaped molecules with two flexible arms (Fig. 11.2). The binding sites are located on the arms and vary from one molecule to another (variable region) [22b]. 

Before details of the structure are given, two important general points about the structure must be emphasised, (a) The B-cell receptor for the antigen shares the same structure as the antibody, (b) Although there are a massive number of different antibodies, the basic structure is the same the variation between the antibodies lies in a small portion of the molecule, the variable region. 

Figure 17.12 Structure of an antibody. V-region is the variable region and C-region is the constant region. Fc is the portion of the antibody that contains the effector domains. S-S is the suLphydryl Link between the chains. NH3 represents the amino terminus of each chain.

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