By Benny K. C. Lo
This booklet offers state-of-the-art suggestions in antibody engineering. partly 1, renowned assets for antibody series research are defined, including in-depth discussions on antibody structural modeling.
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Extra resources for Antibody Engineering, Methods and Protocols
They also suggest that the “sharpness” or “shallowness” of the kink is determined by whether or not the H3:L3 interface is sterically hindered. If it is, the residue at H3:C-3 points toward L2, forming a “sharp” kink, whereas if it is not, it points toward L3, forming a “shallow” kink. However, our studies of an updated set of structures reveal no such correlation. The majority of existing structures conform to the rules of Shirai et al. and Morea et al. There were three exceptions, which were explained by prolines distorting the H3 loop [Protein Databank (PDB) access code: 1mam], positively charged residues in the N-terminal half of the H3 loop, allowing formation of the kink where an extended structure would be expected (1igi), and differing structures in the free and complexed antibodies (1hil).
P. (2000) The human T cell receptor beta diversity (TRBD) and beta joining (TRBJ) genes. Exp. Clin. Immunogenet. 17, 107–114. 30. -P. (1999) Protein displays of the human immunoglobulin heavy, kappa and lambda variable and joining regions. Exp. Clin. Immunogenet. 16, 234–240. 31. -P. (2000) Protein displays of the human T cell receptor alpha, beta, gamma and delta variable and joining regions. Exp. Clin. Immunogenet. 17, 205–215. 32. -P. (1997) Unique database numbering system for immunogenetic analysis.
The results of this analysis are used within the WAM algorithm, but are not detailed here. Of course, readers may use the detailed descriptions of canonical structures and the H3 “rules” in a purely manual fashion. 3. 1. Reclassification of Canonical Loops Our new findings on canonical structures, together with a summary of the rules for each loop, are presented here. For more details of the existing classes, refer to the studies of Chothia and colleagues (12–17). Note that the numbering scheme for some of the classes differs from that used by Chothia and colleagues, but where differences exist they are clearly indicated.
Antibody Engineering, Methods and Protocols by Benny K. C. Lo