Essential Cell Biology 5th edition

How Proteins Are Controlled
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unstructured
region
rapid
collisions
structured
domain
scaffold protein
interacting
proteins
scaffold ready
for reuse
+
protein
complex
Figure 4−52 Scaffold proteins can
concentrate interacting proteins in the
cell. In this hypothetical example, each of
a set of interacting proteins is bound to a
specific structured domain within a long,
otherwise unstructured scaffold protein. The
unstructured regions of the scaffold act as
flexible tethers, and they enhance the rate
of formation of the functional complex by
promoting the rapid, random collision of
the proteins bound to the scaffold.
to them (Figure 4−52). Some other scaffolds are not proteins but long
molecules of RNA. We encounter these RNA scaffolds when we discuss
RNA synthesis and processing in Chapter 7.
Scaffolds allow proteins to be assembled and activated only when and
where they are needed. Nerve cells, for example, deploy large, flexible
scaffold proteins—some more than 1000 amino acids in length—to
organize the specialized proteins involved in transmitting and receiving
the signals that carry information from one nerve cell to the next. These
proteins cluster beneath the plasma membranes of communicating nerve
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cells (see Figure 4–54), allowing them both to transmit and to respond to
the appropriate messages when stimulated to do so.
Weak Interactions Between Macromolecules Can
Produce Large Biochemical Subcompartments in Cells
The aggregates formed by sets of proteins, RNAs, and protein machines
can grow quite large, producing distinct biochemical compartments
within the cell. The largest of these is the nucleolus—the nuclear compartment
in which ribosomal RNAs are transcribed and ribosomal
subunits are assembled. This cell structure, which is formed when the
chromosomes that carry the ribosomal genes come together during interphase
(see Figure 5−17), is large enough to be seen in a light microscope.
Smaller, transient structures assemble as needed in the nucleus to generate
“factories” that carry out DNA replication, DNA repair, or mRNA
production (see Figure 7–24). In addition, specific mRNAs are sequestered
in cytoplasmic granules that help to control their use in protein synthesis.
The general term used to describe such assemblies, many of which contain
both protein and RNA, is an intracellular condensate. Some of
these condensates, including the nucleolus, can take the form of spherical,
liquid droplets that can be seen to break up and fuse (Figure 4–53).
Although these condensates resemble the sort of phase-separated compartments
that form when oil and water mix, their interior makeup is
complex and structured. Some are based on amyloid structures, reversible
assemblies of stacked β sheets that come together to produce a
individual nucleoli
fused nucleoli
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31 min 58 min
10 µm
Figure 4−53 Spherical, liquid-drop-like nucleoli can be seen to fuse in the light microscope. In these experiments, the nucleoli
are present inside a nucleus that has been dissected from Xenopus oocytes and placed under oil on a microscope slide. Here, three
nucleoli are seen fusing to form one larger nucleolus (Movie 4.12). A very similar process occurs following each round of division, when
small nucleoli initially form on multiple chromosomes, but then coalesce to form a single, large nucleolus. (From
C.P. Brangwynne, T.J. Mitchison, and A.A. Hyman, Proc. Natl. Acad. Sci. USA 108:4334–4339, 2011.)
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