Electronegative O has d - charge. H bond acceptor. d + H bond donor.

1. Lynne Regan’s lab in MB&B designs novel proteins to bind to short peptides. One “scaffold” they use is a bundle of alpha helices that form a groove into which a four amino acid peptide ligand can bind. Each amino acid side chain of the ligand is opposed to one amino acid side chain from the scaffold. By genetic engineering, these positions on the scaffold can be changed to any amino acids the protein designer chooses. For this exercise, the goal is to design a scaffold to bind this peptide ligand: RSDF Each group will be assigned one of the four amino acids of the ligand and should design an amino acid to place opposing it on the scaffold. Your group will be asked to say (1) what amino acid you choose for the scaffold and (2) to explain which of the four forces of biochemistry (ionic bond, hydrogen bond, van der Waals interactions, hydrophobic effect) causes interaction(s) with this amino acid that will favor binding. (3) If there is more than one amino acid you could put on the scaffold to get binding, might one work better than another? Why? A table showing the amino acids and their physical properties is given to you to help with this exercise. Electronegative O has d- charge. H bond acceptor. d+ H bond donor.