Experiment 20: Antigenicity
In this lab we are attempting to determine what makes a molecule antigenic and if it is possible to predict which molecules will be more antigenic when compared to others.
Certain characteristics make molecules more antigenic such as the size and the complexity. The larger the molecule, the more antigenic is tends to be and the more complex the more antigenic is tends to be as well. Structural stability of epitopes also contributes to a molecule’s antigenicity. The structure of the molecule needs to be stable. Foreigness is another characteristic where the more different the antigen is, the more antigenic it generally will be. Foreigness is a relative term to the immune system in question. For example an antibody in my immune system is not foreign to me (it is my self), however your immune system will see it as foreign.
There are four characteristics that can be used to determine the type of antigen.
It is possible to predict linear epitopes from amino peptide sequences by computer programs. Discontinuous epitopes are harder to predict because stretched out the epitopes will not connect and often in 3D there is an overlap which complicates matters.
Procedure:
For this lab, we were given two sheets, each had a given protein and a computer layout of its hydrophilicity plot, flexibility plot, and surface probability plot.
Page 1: XX – bovine Rhodopsin (last 106 AA)
Page 2: HGPRT (first 105 AA)
See pages for my predictions. Predictions are on the bottom of each page with the darken blocks being my predicted places to where antigenicity will be the highest.
Discussion
In this lab antigenicity was studied. There are several general characteristics and trends that help predict the antigenicity of a given antigen. These include, but are not limited to, hydrophobicity, flexibility, and surface probability.
Each student was given two unknowns and were told to predict the antigenicity based on the given trends and information. My results can be seen on the worksheet on the previous page. When comparing my predictions with the computer there were places were I did not predict antigenicity to take place. Like all trends, there will always be exceptions and special cases. It is always difficult to determine what is more antigenic than another due to other factors.
The order in which to predict the antigenicty for the given antibody was: