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 JMol 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).