Sajith Jayasinghe
There is an intimate relationship between the three-dimensional structure of a protein and its function. At the most fundamental level, a proteins' three-dimensional structure is the result of various noncovalent interactions (Hydrophobic interactions, hydrogen bonds, electrostatic interactions, and van der Waals forces) formed between the proteins' constituent amino acid side chains, and between the side chains and the environment (specifically water).
The chemical nature of each amino acid side chain determines the extent to which it participates in the various noncavalent forces that help stablize a folded protein.
Let's look at the distribution of amino acids in ubiquitin. In general, the distribution of amino acids within the folded structure should be consistent with the chemical nature of the amino acid side chains.
(1). into the JSMol window (left).
As you highlight each class of amino acid shown below rotate the molecule around and observe the distribution of highlighted residue side chains. After highlighting each class of amino acid answer the two questions that shown below:
Q1. What type of residues are highlighted?
Q2. In general, where in the protein structure are the highlighted residue side chains located? Is the distribution of side chains within the protein consistent with the chemical nature of the side chains highlighted? Briefly justify your answer with reference to the chemical nature of the side chain and the environment it is located.
(2).
(3).
(4).
TUTORIALS: Visualizing the Distribution of Amino Acids in Proteins