Aims

• To reinforce knowledge about the structure and function of antibodies.
• To show examples of engineered proteins.
• To give practice in using molecular graphics software.

Objectives

After this practical you will:

• be familiar with the structure of antibody variable domains;
• be able to identify complementarity determining regions in an antibody structure;
• be aware of the structures of some engineered proteins based on antibodies.

Exercises

1. Protein Data Bank entry 3HFM contains the structure of a complex between an antibody Fab Fragment (HyHEL-10) and lysozyme.

   1. Use the 'restrict' command in RasMol to view only the VH domain of HyHEL-10. Locate the conserved Cys and Trp residues. Compare the main-chain hydrogen bonding pattern with the figure on the handout.

   2. Highlight the six CDR regions in HyHEL-10. What are the sequences of these? Which CDRs are in contact with lysozyme?

2. Protein Data Bank entry 1MOE contains the structure of an engineered diabody.

   1. Identify the chains and domains in this structure. Highlight the CDR regions in this structure.

   2. Locate the linkers in each chain. What are the sequences of these? Comment on the residue types in the linker regions.

3. Protein Data Bank entry 1NMC contains the structure of a complex between a single-chain Fv (scFv) and influenza virus neuraminidase.

   1. Look at the Protein Data Bank and identify the sequence of the linker between the VH and VL domains. The coordinates of the linker are not given in the structure file. With reference to the 3-D structure, approximately where would you expect to find linker?

   2. Highlight the CDR regions in the scFv. Which CDRs are in contact with the virus protein?