Using Molecular Models To Show Steric Clash in Peptides: An Illustration of Two Disallowed Regions in the Ramachandran Diagram

In this activity, students manipulate three-dimensional molecular models of the Ala-Ala-Ala tripeptide, where Ala is alanine. They rotate bonds to show that the pairs of dihedral angles ϕ = 0°, ψ = 180°, and ϕ = 0°, ψ = 0° lead to unfavorable interactions among the main chain atoms of the tripeptide. This activity allows the student to visualize in three dimensions why these two pairs of dihedral angles fall within the disallowed region of the Ramachandran diagram, a fundamental tool in the understanding and teaching of protein structure. The advanced activity introduces biochemistry students to unfavorable interactions of the β carbon of the side chain.