Abstract

To analyze the differential length of linkers of peptides on the conformation of single-chain antibody, and seek the length of linkers with which the conformation is the most similar to the wild type antibody. The similarity between the wild type antibody model and the single-chain antibody model was calculated by the comparison method of spherical shell layer; after comparing with conclusions of other algorithms, the length of the linker (connecting peptide) with which does little influence on the conformation of heavy chain variable (VH) and light chain variable (VL) of single-chain antibody was obtained. The similarity value was got when the number of layers range from 2 to 2000 and the length of the linker range from 0 to 9 by the method of layered spherical coordinate-based algorithm for similarity, and the average values ​​were 0.84974, 0.84101, 0.84970, 0.84532, 0.84285, 0.84235, 0.84077, 0.83857, 0.84237 and 0.83905 when n is equal to 0, 1, 2, 3, 4, 5, 6, 7, 8, 9. The VH and VL of the single-chain antibody gain little influence on the conformation when n = 0 (n is even) and n = 3 (n is odd). When the length of G4S linker (n value) is 3, the influence on the conformation of single-chain antibody is least.

Key word: Single-chain antibody, spherical coordinates, similarity, conformation and linker.