Page 77 - Color Atlas of Biochemistry

68 Biomolecules
Secondary structures
In proteins, specific combinations of the dihe-
dral angles φ and ψ (see p. 66) are much more
common than others. When several succes-
sive residues adopt one of these conforma-
tions, defined secondary structures arise,
which are stabilized by hydrogen bonds ei-
ther within the peptide chain or between
neighboring chains. When a large part of a
protein takes on a defined secondary struc-
ture, the protein often forms mechanically
stable filaments or fibers. Structural proteins
of this type (see p. 70) usually have character-
istic amino acid compositions.
The most important secondary structural
elements of proteins are discussed here first.
The illustrations only show the course of the
peptide chain; the side chains are omitted. To
make thecourseof the chains clearer, the
levels of the peptide bonds are shown as
blue planes. The dihedral angles of the struc-
tures shown here are also marked in diagram
D1 on p. 67.
A. D-Helix
The right-handed α-helix (α R )is one of the
most common secondary structures. In this
conformation, the peptide chain is wound
like a screw. Each turn of the screw (the screw p. 71 C). The β a structure, with its almost lin-
axis in shown in orange) covers approxi-
mately 3.6 amino acid residues. The pitch of
the screw (i. e., the smallest distance between strands of the sheet are usually not parallel,
two equivalent points) is 0.54 nm. α-Helices
are stabilized by almost linear hydrogen bonds
between the NH and CO groups of residues,
which are four positions apart from each an-
other in the sequence (indicated by red dots;
see p. 6). In longer helices, most amino acid
residuesthusenter into two Hbonds.Apolar
or amphipathic α-helices with five to seven
turns often serve to anchor proteins in bio-
logical membranes (transmembrane helices;
see p. 214).
The mirror image of the α R helix, the left- Both are stabilized by hydrogen bonds be-
handed D-helix (α L ), is rarely found in nature, tween residues 1 and 4. β Turns are often
although it would be energetically “permissi-
ble.”
Koolman, Color Atlas of Biochemistry, 2nd edition © 2005 Thieme
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B. Collagen helix
Another type of helix occurs in the collagens,
which are important constituents of the con-
nectivetissue matrix (see pp. 70, 344). The
collagen helix is left-handed,and with a pitch
of 0.96 nm and 3.3 residues per turn, it is
steeper than the α-helix. In contrast to the
α-helix, H bonds are not possible within the
collagen helix. However, the conformation is
stabilized by the association of three helices
to form a righthanded collagen triple helix
(see p. 70).
C. Pleated-sheet structures
Two additional, almost stretched, conforma-
tions of the peptide chain are known as E
pleated sheets, as the peptide planes are ar-
ranged like a regularly folded sheet of paper.
Again, H bonds can only form between neigh-
boring chains (“strands”) in pleated sheets.
When the two strands run in opposite direc-
tions (1), the structure is referred to as an
antiparallel pleated sheet (β a ). When they
runinthe same direction(2), it is a parallel
pleated sheet (β p ). In both cases, the α-C
atoms occupy the highest and lowest points
in the structure, and the side chains point
alternately straight up or straight down (see
ear H bonds, is energetically more favorable.
In extended pleated sheets, the individual
but twisted relative to one another (see p. 74).
D. E Turns
E Turns are often found at sites where the
peptide chain changes direction. These are
sections in which four amino acid residues
are arranged in such a way that the course
of the chain reverses by about 180° into the
opposite direction. The two turns shown
(types I and II) are particularly frequent.
located between the individual strands of
antiparallel pleated sheets, or between
strands of pleated sheets and α helices.