Abstract
A biophysical chemistry laboratory project is described that combines classroom and laboratory experiences to design and characterize a Zn2+-binding four-helix bundle protein. The design phase involves re-examining principles of protein structure and function in the context of four-helix bundle literature and then using the online computer game Foldit to build and optimize a 35-residue helix-loop-helix peptide that would coordinate Zn2+. The designed peptide and a control peptide containing the same amino acids but in a random sequence are purchased commercially. The peptides are then characterized by native polyacrylamide gel electrophoresis, immobilized-metal affinity chromatography, and 1H NMR spectroscopy. The results indicate that the designed peptide adopts a higher-order structure than the control peptide, although not conclusively a four-helix bundle, and that it also binds Zn2+.