You are now going to take the two protein sequences and predict the secondary structure of the proteins by using a tool called "GOR4". This tool will show the sequence of each protein and color code alpha helices with the color red and beta sheets with the color blue, according to where they are found in the protein sequence. We will use this tool to see if the mutated amino acid has caused a conformational change in the mutant sequence when compared to the wild type sequence.

1. Go back to the Protein Tools homepage. You can do this by scrolling to the bottom of the screen and clicking on "Return".



2. Make sure that there are check marks in the boxes next to the sequences. Highlight the choice that says "GOR4 ¡V Predict Secondary Structure of PS". Once this choice is highlighted, click on "Run".



Now you will be brought to a new screen. Just click on "Submit".



A new screen will appear and your results will be shown:



The top sequence is the wild type (you tell this by looking at the code "1lpe" compared to the mutant sequence found on the bottom; "1le2". If you will look at the legend found below the sequences, you will see that alpha helices are colored red and beta sheets are colored blue.

3. Now, count the number of alpha helices and beta sheets in the wild type protein sequence and in the mutant protein sequence. If you counted correctly, there are 5 alpha helices and 1 beta sheet in the wild type. However, there are 5 alpha helices and 2 beta sheets in the mutant sequence. Some of the helical structure of the wild-type protein has been changed to beta sheet structure. This tells us that the point mutation in the mutant protein sequence has caused a subtle conformational change in the protein structure. Next we'll do one last experiment, to see if we can determine why the protein structure might be affected in the mutant.