Essential Cell Biology 5th edition

124 CHAPTER 4 Protein Structure and Function
newly synthesized,
partially folded proteins
chamber
cap
chaperone
protein
one polypeptide
chain is sequestered
by the chaperone
isolated
polypeptide
chain folds
correctly
correctly folded
protein is released
when cap
dissociates
Figure 4–9 Some chaperone proteins act as isolation chambers that help a
polypeptide fold. In this case, the barrel of the chaperone provides an enclosed
chamber in which a newly synthesized polypeptide chain can fold without the risk of
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aggregating with other polypeptides in the crowded conditions of the cytoplasm.
This system also requires an input of energy from ATP hydrolysis, mainly for the
association and subsequent dissociation of the cap that closes off the chamber.
Proteins Come in a Wide Variety of Complicated Shapes
Proteins are the most structurally diverse macromolecules in the cell.
Although they range in size from about 30 amino acids to more than
10,000, the vast majority are between 50 and 2000 amino acids long.
Proteins can be globular or fibrous, and they can form filaments, sheets,
rings, or spheres (Figure 4−10). We will encounter many of these structures
throughout the book.
To date, the structures of about 100,000 different proteins have been
determined (using techniques we discuss later in the chapter). Most proteins
have a three-dimensional conformation so intricate and irregular
that their structure would require the rest of the chapter to describe in
detail. But we can get some sense of the intricacies of polypeptide structure
by looking at the conformation of a relatively small protein, such as
the bacterial transport protein HPr.
This small protein, only 88 amino acids long, facilitates the transport
of sugar into bacterial cells. In Figure 4−11, we present HPr’s threedimensional
structure in four different ways, each of which emphasizes
different features of the protein. The backbone model (see Figure 4−11A)
shows the overall organization of the polypeptide chain and provides a
straightforward way to compare the structures of related proteins. The
ribbon model (see Figure 4−11B) shows the polypeptide backbone in a
way that emphasizes its most conspicuous folding patterns, which we
describe in detail shortly. The wire model (see Figure 4−11C) includes the
positions of all the amino acid side chains; this view is especially useful
for predicting which amino acids might be involved in the protein’s activity.
Finally, the space-filling model (see Figure 4−11D) provides a contour
map of the protein surface, which reveals which amino acids are exposed
on the surface and shows how the protein might look to a small molecule
such as water or to another macromolecule in the cell.
The structures of larger proteins—or of multiprotein complexes—are even
more complicated. To visualize such detailed and intricate structures,
scientists have developed various computer-based tools to emphasize
different features of a protein, only some of which are depicted in
Figure 4–11. All of these images can be displayed on a computer screen
and readily rotated and magnified to view all aspects of the structure
(Movie 4.1).
When the three-dimensional structures of many different protein molecules
are compared, it becomes clear that, although the overall