Variable domain

Several silk fibroin genes have been cloned and sequenced and they all show a similar sequence pattern variable domains at the N- and C-termini flank a large region of repetitive short sequences of alternating poly-Ala (8 to 10 residues) and Gly-Gly-X repeats (where X is usually Ser, Tyr, or Gin). This middle region varies in length and may comprise up to 800 residues. 

The most remarkable feature of the antibody molecule is revealed by comparing the amino acid sequences from many different immunoglobulin IgG molecules. This comparison shows that between different IgGs the amino-terminal domain of each polypeptide chain is highly variable, whereas the remaining domains have constant sequences. A light chain is thus built up from one amino-terminal variable domain (Vl) and one carboxy-terminal constant domain (Cl), and a heavy chain from one amino-terminal variable domain (Vh), followed by three constant domains (Chi, Ch2. and Chs). 

The overall structure of the variable domain is very similar to that of the constant domain, hut there are nine p strands instead of seven. The two additional p strands are inserted into the loop region that connects p strands C and D (red in Figure 15.8). Functionally, this part of the polypeptide chain is important since it contains the hypervariahle region CDR2. The two extra p strands, called C and C", provide the framework that positions CDR2 close to the other two hypervariahle regions in the domain structure (Figure 15.8). 

The hypervariahle regions are clustered in loop regions at one end of the variable domain... 

The variable domains associate in a strikingly different manner. It is obvious from Figure 15.11 that if they were associated in the same way as the constant domains, via the four-stranded p sheets, the CDR loops, which are linked mainly to the five-stranded p sheet, would be too far apart on the outside of each domain to contribute jointly to the antigen-binding site. Thus in the variable domains the five-stranded p sheets form the domain-domain interaction area (Figure 15.11). Furthermore, the relative orientation of the p strands in the two domains is closer to parallel than in the constant domains and the curvature of the five-stranded p sheets is such that they do not pack... 

Figure 15.12 Schematic diagram of the barrel arrangement of four p strands from each of the variable domains in Fab. The six hypervariable regions, CDR1-CDR3 from the light chain (L1-L3) and from the heavy chain (H1-H3), are at one end of this barrel. (From J. Novotny et al., /. Biol. Chem. 2S8 14433-14437, 1983.)...

IgG antibody molecules are composed of two light chains and two heavy chains joined together by disulfide bonds. Each light chain has one variable domain and one constant domain, while each heavy chain has one variable and three constant domains. All of the domains have a similar three-dimensional structure known as the immunoglobulin fold. The Fc stem of the molecule is formed by constant domains from each of the heavy chains, while two Fab arms are formed by constant and variable domains from both heavy and light chains. The hinge region between the stem and the arms is flexible and allows the arms to move relative to each other and to the stem. 

The constant domain has a stable framework structure composed of two antiparallel sheets comprising seven p strands, four in one sheet and three in the other. The variable domains have a similar framework structure but comprising nine p strands, five in one sheet and four in the other. The three hypervariable regions are in loops at one end of the variable domain. The variable domains from the heavy and light chains associate through their five-stranded p sheets to form a barrel with the hypervariable loop regions from both domains close together at the top of the barrel. 

Chothia, C., et al. Domain association in immunoglobulin molecules. The packing of variable domains. /. Mol. Biol. 186 651-663, 1985. 

A number of chimerized, humanized, and one human mAb have now been approved for therapeutic use in humans in the treatment of autoimmunity, malignancy, infection and cardiovascular disease (Table 1). Some of the currently licensed mAb will be discussed here. A much larger number of mAb are currently being evaluated in Phase I, II and III trials. In general, chimeric, humanized and human mAb are very well tolerated with few side effects. Chimeric or humanized mAb still have the potential to evoke host immune response to the variable domains or CDRs of the antibody so-called HACA (human anti-chimeric antibody) or HAHA (human anti-human antibody) responses, although these responses are uncommon. Short-lived and occasionally severe infusion-related acute hypersensitivity reactions such as fever, skin itching, shivering, respiratory compromise and low blood pressure sometimes occur-. Such effects may... 

Stevens PW, Raffen R, Hanson DK, Deng YL, Berrios Hammond M, Westholm FA, Murphy C, Eulitz M, Wetzel R, Solomon A, et al. Recombinant immunoglobulin variable domains generated from synthetic genes provide a system for in vitro characterization of light-chain amyloid proteins. Protein Sci 1995 4 421-432. 

Orlandi, R., Gussow, D.H., Jones, P.T., and Winteg G. (1989) Cloning immunoglobulin variable domains for expression by the polymerase chain reaction. Proc. Natl. Acad. Sci. USA 86, 3833-3837. 

Figure 4.10 (a) The Cu-Zn superoxide dismutase is made up of eight anti-parallel P-strands both the constant (b) and variable (c) domains of immunoglobulins are made up of seven anti-parallel P-strands with the same topology the variable domain contains two additional P-strands. (From Branden and Tooze, 1991. Reproduced by permission of Garland Publishing, Inc.)... 

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