In order to visualize our engineered protein we built the protein on the computer using a program called Pymol. By building the protein in Pymol first we were able to visualize placement and size of the protein pieces.
The first step to building our protein was to find the PDB files of each protein piece on the protein data bank. These files were both uploaded to Pymol. The rapamycin complex PDB code is 1fap and the PD1 antibody complex code is 5ggs.
First the PD1 5ggs file was uploaded into Pymol. The crystal structure included multiple antibody structures. In order to visualize the antibody more clearly a single antibody was isolated.
Then the bottom two immunoglobulin units of the antibody were removed.
The rapamycin complex was attached to the bottom of the immunoglobulin units to replace the bottom immunoglobulin units. two short linkers were created between the top immunoglobulin units and the rapamycin complex and one long linker was created to attach the two chains of the new antibody. Currently, the small linkers are made up of Glycine-Serine-Glycine and the long linker is made up of the repeating sequence Glycine-Glycine-Serine with a protease cleavage site in the middle.
Currently we are working on measuring the energies of our protein with different sized linkers in order to find the most stable sized linker. We are using the programs VMD and NAMD for our simulations.
Back to Top