Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

THE SHAPE AND STRUCTURE OF PROTEINS
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framework for many elongated proteins. Examples are α-keratin, which forms the
intracellular fibers that reinforce the outer layer of the skin and its appendages,
and the myosin molecules responsible for muscle contraction.
Protein Domains Are Modular Units from Which Larger Proteins
Are Built
Even a small protein molecule is built from thousands of atoms linked together by
precisely oriented covalent and noncovalent bonds. Biologists are aided in visualizing
these extremely complicated structures by various graphic and computer-based
three-dimensional displays. The student resource site that accompanies
this book contains computer-generated images of selected proteins, displayed
and rotated on the screen in a variety of formats.
Scientists distinguish four levels of organization in the structure of a protein.
The amino acid sequence is known as the primary structure. Stretches of polypeptide
chain that form α helices and β sheets constitute the protein’s secondary
structure. The full three-dimensional organization of a polypeptide chain is
sometimes referred to as the tertiary structure, and if a particular protein molecule
is formed as a complex of more than one polypeptide chain, the complete
structure is designated as the quaternary structure.
Studies of the conformation, function, and evolution of proteins have also
revealed the central importance of a unit of organization distinct from these four.
This is the protein domain, a substructure produced by any contiguous part of
a polypeptide chain that can fold independently of the rest of the protein into a
compact, stable structure. A domain usually contains between 40 and 350 amino
acids, and it is the modular unit from which many larger proteins are constructed.
The different domains of a protein are often associated with different functions.
Figure 3–10 shows an example—the Src protein kinase, which functions in
signaling pathways inside vertebrate cells (Src is pronounced “sarc”). This protein
(A)
(B)
Figure 3–8 Two types of β sheet
structures. (A) An antiparallel β sheet (see
Figure 3–7C). (B) A parallel β sheet. Both of
these structures are common in proteins.
MBoC6 m3.08/3.08
a
NH 2
NH 2 NH 2
d
e
a
d
e
g
g
c
c
g
d
g
d
a
d
0.5 nm
a
a
stripe of
hydrophobic
“a” and “d”
amino acids
11 nm
helices wrap around each other to minimize
exposure of hydrophobic amino acid
side chains to aqueous environment
HOOC
(A) (B) (C)
COOH
Figure 3–9 A coiled-coil. (A) A single α
helix, with successive amino acid side
chains labeled in a sevenfold sequence,
“abcdefg” (from bottom to top). Amino
acids “a” and “d” in such a sequence lie
close together on the cylinder surface,
forming a “stripe” (green) that winds
slowly around the α helix. Proteins that
form coiled-coils typically have nonpolar
amino acids at positions “a” and “d.”
Consequently, as shown in (B), the two α
helices can wrap around each other with
the nonpolar side chains of one α helix
interacting with the nonpolar side chains
of the other. (C) The atomic structure
of a coiled-coil determined by x-ray
crystallography. The alpha helical backbone
is shown in red and the nonpolar side
chains in green, while the more hydrophilic
amino acid side chains, shown in gray, are
left exposed to the aqueous environment
(Movie 3.4). (PDB code: 3NMD.)