Effect of Electrostatic Interactions on Folding

1. Effect of Electrostatic Interactions on Folding Now that you have manipulated charges to view their attractive and repellant properties based on charge we will look at how these charges can effect the folding of a protein Go to http://workbench.concord.org/database/activities/213.html Click on “go to activity” Using the worksheet provided investigate protein folding and answer the questions provided

2. Bioinformatics: Protein Folding Name: ______________________ Pd:_____ http://workbench.concord.org/database/activities/213.html Once the page is loaded play both the original chain and the alternately charged chain. Change arganine to lysine on the last three red arganine molecules and then skip three more arganine from the end and change the next three (the 7th, 8th and 9th molecules from the end of the chain) to lysine as well. 1. How does this change the protein formation? Why? Reset the model Change arganine to aspartic acid on the last three red arganine molecules and then skip three more arganine from the end and change the next three (the 7th, 8th and 9th molecules from the end of the chain) to aspartic acid as well. 2. How does this change the protein formation? Why? Do not reset the model Now change the first 6 of the arganine chain ( the ones closest to the glutamic acid chain ) to valine. 3. How does this change the protein formation? 4. Which change (arganine to aspartic acid or arganine to valine) do you believe caused the biggest change in the folding of the protein? Why? Go to: http://cnx.org/content/m11467/latest/ Read the introduction and the section titled misfolding 5. What is the importance of protein folding on protein function?