Lecture 37. Part I: Protein Structure.
Ed; pp. 313, 366 + Fig 19.10 7
Ed.; pp. 319, 380
Part II: Cancer.
Ed.; pp. 368-371 7
Especially for this lecture, where the PowerPoint slides have a lot of pictures, your should refer to
the appropriate slides while you’re going through these notes.
Part I: Structural biology
is the branch of biology concerned with figuring out the 3-
dimensional structures of macromolecules. These days, most work is being done on proteins.
Techniques like X-ray crystallography (used in the 1950’s to determine the structure of DNA) are
very valuable for determining the structures of proteins even today. This is because each protein
has a different structure, and it’s not possible to predict the structure of an entire protein by looking
at its amino acid sequence.
Proteins often (but not always!) consist of separate domains that fold independently (see 7
Ed., Fig. 17.12). In some cases, these domains are encoded by separate exons. Each domain can
contain combinations of different secondary structure elements:
elements are arranged in a characteristic shape in each type of domain. That is, the hallmark of
each domain is a characteristic 3-D shape. Different domains in one protein can have independent
functions. For instance, one domain might have enzymatic activity (such as kinase activity), while
another domain functions to bind another protein. Furthermore, the same domain is often found in
different proteins. That is, proteins can be mix-and-match combinations of different domains. For
instance, “Protein #1” may consist of 3 domains; A, B, and C. “Protein #2” may consist of 4
domains; 2 copies of A, B, and D. In this case, domains A and B are present in both proteins, while
domains C and D are only in one of them. The same domain will have the same overall shape in the
different proteins. In our example, we’ll be able to recognize a “Domain A” in both Protein #1 and
Protein #2. In addition, the amino acid sequences of Domain A in the two proteins will probably be
very similar. However, they won’t be identical. As we’ll see, small changes in the same domain
found in two different proteins can have important consequences for function.
We’ll look at two examples of common domains, that are both found in many different
proteins. Both are involved in binding to other proteins. The first, called the SH2 domain, binds
phosphorylated tyrosine residues (P-Tyr). The second, called the helix-turn-helix (HTH) domain,
Example #1: SH2 domains
. A small tyrosine kinase called Src has 3 domains. In order,
starting at the amino (N-) terminus of the protein, these are the SH3, SH2, and kinase domains.
(The kinase domain technically consists of two separate domains: the small kinase domain and large