Biochemistry Lecture No. 5: Protein Function
Friday September 14 , 2012
-Many proteins consist of more than one polypeptide and are known for possessing a quaternary
structure as a result. The forces/bonds involved in quaternary structures are the same as for tertiary
structures (Hydrophobic, H-bonds, van der Waals, ionic, disulfide bonds). Subunits are the individual
polypeptide chains within a quaternary structure. For example, the P53 tetramer, mutated in about 50%
of cancers, is comprised of 4 subunits that form a quaternary structure.
-A type of quaternary structure is the coiled coil, whose repeating sequence plays a very important role
in its structure. With a repeating pattern every 7 resides, helices wrap around one another to minimize
exposure of hydrophobic residues to the aqueous environment, leaving what is called a hydrophobic
stripe on one side of the helix. Examples of proteins containing the coiled coil structure are EB1, which
binds to microtubule ends and GCN4 which is a transcription factor.
Indication Of Protein Structure In Biochemistry:
-Biochemists indicate protein structure using three distinct models: wire, ribbon and space-filling. In the
wire visualization, side chains and their respective proximity are represented in order to predict amino
acids involved in function. In the ribbon model, secondary structures are primarily represented. In the
space-filling representation, one can visualize the specific shape of the protein, which amino acids are
on the surface, as well as predict possible interactions with water or proteins.
-After a protein has been translated into its linear sequence and has achieved its 3D conformation, it can
experience one of the following post-translational modifications: the binding of lipids (to form a
lipoprotein), the binding of metal ions (to form a metalloprotein), and the binding of a heme group (to
form a hemeprotein). Another possible modification is the phosphorylation of a protein, which affects
its ultimate function.
-Although this is area of molecular biology is greatly mysterious, it is now widely believed that molecular
chaperones, proteins that help other proteins achieve their 3D conformation (native state), are primarily
responsible for driving protein folding in cells. Conformational Flexibility & Changes:
-Proteins are not completely rigid structures and various types of motion are possible depending on
their structure. It is often domains that can move, connected by flexible linkers. These adjustments in
the protein’s make-up are known as conformational changes and many such changes a