Essential Cell Biology 5th edition

The Shape and Structure of Proteins
127
(A)
(B)
β sheet
R
R
R
R
R
R
oxygen
R
peptide
bond
R
R
R
carbon
nitrogen
R
R
R
carbon
hydrogen
hydrogen
bond
R
R
amino acid
side chain
Figure 4−13 Some polypeptide chains
fold into an orderly pattern called a
β sheet. (A) In a β sheet, several segments
(strands) of an individual polypeptide chain
are held together by hydrogen-bonding
between peptide bonds in adjacent
strands. The amino acid side chains in
each strand project alternately above
and below the plane of the sheet. In the
example shown, the adjacent chains run in
opposite directions, forming an antiparallel
β sheet. All of the atoms in the polypeptide
backbone are shown; the amino acid side
chains are denoted by R. (B) The same
polypeptide, showing only the carbon
(black and gray) and nitrogen (blue) atoms.
(C) Cartoon symbol used to represent
β sheets in ribbon models of proteins (see
Figure 4−11B).
QUESTION 4–2
(C)
0.7 nm
Helices Form Readily in Biological Structures
The abundance of helices in proteins is, in a way, not surprising. A helix
ECB5 4.13D-F/4.13.5
is generated simply by placing many similar subunits next to one another,
each in the same strictly repeated relationship to the one before. Because
it is very rare for subunits to join up in a straight line, this arrangement
will generally result in a structure that resembles a spiral staircase
(Figure 4−14). Depending on the way it twists, a helix is said to be either
right-handed or left-handed (see Figure 4−14E). Handedness is not
affected by turning the helix upside down, but it is reversed if the helix is
reflected in a mirror.
(A) (B) (C) (D)
lefthanded
(E)
righthanded
Remembering that the amino
acid side chains projecting from
each polypeptide backbone in a
β sheet point alternately above
and below the plane of the sheet
(see Figure 4−13A), consider
the following protein sequence:
Leu-Lys-Val-Asp-Ile-Ser-Leu-Arg-
Leu-Lys-Ile-Arg-Phe-Glu. Do you
find anything remarkable about the
arrangement of the amino acids in
this sequence when incorporated
into a β sheet? Can you make any
predictions as to how the β sheet
might be arranged in a protein?
(Hint: consult the properties of the
amino acids listed in Figure 4−3.)
Figure 4−14 A helix is a common, regular,
biological structure. A helix will form when
a series of similar subunits bind to each
other in a regular way. At the bottom, the
interaction between two subunits is shown;
behind them are the helices that result.
These helices have (A) two, (B) three, or
(C and D) six subunits per helical turn. At
the top, the arrangement of subunits has
been photographed from directly above the
helix. Note that the helix in (D) has a wider
path than that in (C), but the same number
of subunits per turn. (E) A helix can be either
right-handed or left-handed. As a reference,
it is useful to remember that standard
metal screws, which advance when turned
clockwise, are right-handed. So to judge the
handedness of a helix, imagine screwing it
into a wall. Note that a helix preserves the
same handedness when it is turned upside
down. In proteins, α helices are almost
always right-handed.