Hypervariable loops

RM Fine, H Wang, PS Shenkm, DL Yarmush, C Levmthal. Predicting antibody hypervariable loop conformations. II Minimization and molecular dynamics studies of MCP603 from many randomly generated loop conformations. Proteins 1 342-362, 1986. 

ACR Martin, JC Cheetham, AR Rees. Modeling antibody hypervariable loops A combined algorithm. Proc Natl Acad Sci USA 86 9268-9272, 1989. 

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. 

Bruccoleri, R.E., Haber, E., Novotny, J. 5tructure of antibody hypervariable loops reproduced by a conformational search algorithm. Nature 335 564-568, 1988. 

Tomlinson, I.M., Walter, G., Marks, J.D., et al. (1992). The repertoire of human germline VH sequences reveals about fifty groups of VH segments with different hypervariable loops. J. Mol. Biol., 227, 776-798. 

The amino acid sequence of the hypervariable loop is determined, and homology modelling then used to find a plausible secondary structure (Martin et al., 1989). 

Key amino acids in the hypervariable loops of Ab-2 are found by homology matching with sequences in the original macromolecular antigen (Williams et al., 1988). 

Foote J, Winter G. 1992. Antibody framework residues affecting the conformation of the hypervariable loops. J Mol biol. 224 487 199. 

R. M. Fine. P. S- Wang, D. L. shenkin1 D. Yarmush, and C. LeviiuhaL Predicting antibody hypervariable loop conformations II Minimization and molecular dynamics... 

Thompson J, Pope T, Tung JS, Chan C, Hollis G, Mark G, Johnson KS, Affinity maturation of a high-affinity human monoclonal antibody against the third hypervariable loop of human immunodeficiency virus use of phage display to improve affinity and broaden strain reactivity, J. Mol. Biol., 256 77-88, 1996. 

P. S. Shenkin, D. L. Yarmush, R. M. Fine, H. Wang, and C. Levinthal, Biopolymers, 26, 2053 (1987). Predicting Antibody Hypervariable Loop Conformation. I. Ensembles of Random Conformations for Ringlike Structures. 

The Immunoglobulin Fold Consists of a Beta-Sandwich Framework with Hypervariable Loops... 

Figure 33.9. Immunoglobulin Fold. An immunoglobulin domain consists of a pair of P-sheets linked by a disulfide bond and hydrophobic interactions. Three hypervariable loops lie at one end of the structure.

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