Single chain antibody structural alignment

Protocol

There are four steps to compare structure of single chain antibody and FGF binding domain of FGFR. First step is taking variable region sequences of antibodies. Next step is combining these variable region sequences with linker sequence to make single chain antibody sequence. Third step is predicting the structure of single chain antibody with structure prediction program like modeler. Final step is to structural align these structures of antibodies with structure of FGF binding domain of FGFR(PDB ID : 1EVT).

Data source

Single chain antibody is the combination of variable regions of known antibodies with linker sequence which can bind to the antigens. We need to know the V_L and V_H sequences to make single chain antibody. The source of these antibody sequences are NCBI, Uniprot and RCSB PDB. NCBI and Uniprot provide the single chain sequence of variable regions (V_L and V_H) and antigen binding fragments (F_ab). RCSB provide the structure of the complexes of antigenbinding fragment which binds to its antigens. But we only need the sequence of variable region. So we get the last 120~150 reside and assume them as the variable region. And data from RCSB contain not only sequence of antibody, but also antigens. S we filter them based on label of files.to get heavy chains and light chains of antibody.

Single chain antibody synthesis

We combine the antibody variable region sequences with order of V_H-linker-V_L to make single chain antibody sequence. The sequence of linker is GGGGSGGGGS

Structure Prediction

We used the Modeller program to predict the structure of single chain antibody from its sequence. Modeller predict 3D structure of protein with structure of know similar proteins based on homology model. Input file is the sequence of single chain antibody with fasta format and output file is the structure of single chain antibody with pdb format.

Structure Alignment

Result

Result Analysis