Question

Protein structures are displayed in several ways, including: spacefilling models, ball and stick models, stick models, backbone models (which show the n-calpha-c=o units) and the cartoon representation (which shows the secondary structures).

Choose the best representations for each and EXPLAIN why:

1) Channels, holes, or pockets in a protein.

2) Secondary structures present in a molecule.

3) Residues in the active site of an enzyme.

EXPLAIN your choice for each.

Answer 1

1. Ball and stick model can be used to study channels, holes or pockets in a protein. It perfectly represents the angle between the bonds. This helps in determining the size of the pockets and holes and helps in determining size of the substance fitting in it.

2. Secondary structure can be best studied with spacefilling model. Space filling model is a three dimentional molecular model where atoms are represented by spheres whose radii is proportional to the radii of the atom. Different colour is used to represent different atoms.

3. Ribbon cartoon model is best to study residues in the active site of the enzyme. This gives a better picture as to where the active site might be located on the protein and what are the possible interacting ligands.