By Benny K. C. Lo
This booklet provides state-of-the-art options in antibody engineering. partially 1, renowned assets for antibody series research are defined, including in-depth discussions on antibody structural modeling.
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Any apparent similarities were subsequently verified by calculating the global RMSD between each H3 loop. When similarities were observed, a search was made for possible canonical-type features, such as hydrogen bond, salt bridge, and hydrophobic interactions, using both visual examination for identification and the CONTACT program (N. Whitelegg, unpublished results) to analyze and list probable interactions of those types. For exceptions in a length class that exhibited a similar conformation to the remaining members, the same methods were used to search for interactions that might be responsible for the unusual conformation.
Class 2 and New Class 6 (11 Residues) Of the 59 occurrences of 11-residue L1s, only 40 fit the canonical sequence rules for class 2, whereas all but two are members of the class on conformational grounds. The two exceptions—8fab and 1nfd—both contain a Pro at residue Antibody Variable Regions 59 Fig. 1A. The contrasting conformations of 10-residue L1 loops of class 1 (1vfa, left) and class 6 (8fab, right). Fig. 1B. Top: 16-residue L1 loops. Left: 1dba, an example of a 16-residue L1 loop with the defining class 4 interaction; right, 1axt, an example of a 16-residue L1 loop that cannot form the class 4 interaction as a result of steric effects.
33. -P. (1999) The IMGT unique numbering for Immunoglobulins, T cell receptors and Ig-like domains. The Immunologist 7, 132–136. 34. Kabat, E. , Wu, T. , Perry, H. , Gottesman, K. , and Foeller, C. (1991) Sequences of proteins of immunological interest. , pp. 91–3242. 35. , Cohen, G. , Padlan, E. , and Davies, D. R. (1986) Phosphocholine binding immunoglobulin Fab McPC603. J. Mol. Biol. 190: 593–604. 36. Chothia, C. and Lesk, A. M. (1987) Canonical structures for the hypervariable regions of immunoglobulins.
Antibody Engineering, Methods and Protocols by Benny K. C. Lo