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

116 Chapter 3: Proteins
R
R
carbon
R
R
R
R
R
R
amino acid
side chain
R
oxygen
H-bond
hydrogen
nitrogen
0.54 nm
carbon
nitrogen
carbon
nitrogen
R
peptide
bond
R
H-bond
hydrogen
oxygen
R
R
R
R
R
R
R
R
R
carbon
amino acid
side chain
R
0.7 nm
(A)
(B)
R R R
(C)
(D)
Figure 3–7 The regular conformation of the polypeptide backbone in the α helix and the β sheet. The α helix is shown in
(A) and (B). The N–H of every peptide bond is hydrogen-bonded to the C=O of a neighboring peptide bond located four peptide
bonds away in the same chain. Note that all of the N–H groups point up in this diagram and that all of the C=O groups point
down (toward the C-terminus); this gives a polarity to the helix, with the C-terminus having a partial negative and the N-terminus
a partial positive charge (Movie 3.2). The β sheet is shown in (C) and (D). In this example, adjacent peptide chains run in
opposite (antiparallel) directions. Hydrogen-bonding between peptide bonds in different strands holds the individual polypeptide
chains (strands) together in a β sheet, and the amino acid side chains in each strand alternately project above and below the
plane of the sheet (Movie 3.3). (A) and (C) show all the atoms in the polypeptide backbone, but the amino acid side chains are
truncated and denoted by R. In contrast, (B) and (D) show only the carbon and nitrogen backbone atoms.
MBoC6 m3.07/3.07
The cores of many proteins contain extensive regions of β sheet. As shown
in Figure 3–8, these β sheets can form either from neighboring segments of the
polypeptide backbone that run in the same orientation (parallel chains) or from
a polypeptide backbone that folds back and forth upon itself, with each section
of the chain running in the direction opposite to that of its immediate neighbors
(antiparallel chains). Both types of β sheet produce a very rigid structure,
held together by hydrogen bonds that connect the peptide bonds in neighboring
chains (see Figure 3–7C).
An α helix is generated when a single polypeptide chain twists around on itself
to form a rigid cylinder. A hydrogen bond forms between every fourth peptide
bond, linking the C=O of one peptide bond to the N–H of another (see Figure
3–7A). This gives rise to a regular helix with a complete turn every 3.6 amino acids.
The SH2 protein domain illustrated in Figure 3–6 contains two α helices, as well as
a three-stranded antiparallel β sheet.
Regions of α helix are abundant in proteins located in cell membranes, such
as transport proteins and receptors. As we discuss in Chapter 10, those portions
of a transmembrane protein that cross the lipid bilayer usually cross as α helices
composed largely of amino acids with nonpolar side chains. The polypeptide
backbone, which is hydrophilic, is hydrogen-bonded to itself in the α helix and
shielded from the hydrophobic lipid environment of the membrane by its protruding
nonpolar side chains (see also Figure 3–75A).
In other proteins, α helices wrap around each other to form a particularly stable
structure, known as a coiled-coil. This structure can form when the two (or in
some cases, three or four) α helices have most of their nonpolar (hydrophobic)
side chains on one side, so that they can twist around each other with these side
chains facing inward (Figure 3–9). Long rodlike coiled-coils provide the structural