Download The linear sequence of amino acids (primary structure) is able to coil

The linear sequence of amino acids (primary structure) is able to coil and fold upon itself, resulting in 3D
formations such as α-helices and β-sheets. These are held together by hydrogen bonding between
amino acids. The term for these 3D formations is the secondary structure of the protein.
Secondary structural features are held
together by hydrogen bonds between an
oxygen lone pair of one amino acid and
the hydrogen attached to the nitrogen of
another. In proteins, the hydrogen bonds
are always between C=O and N-H groups.
H-bond
What makes the structural features
different is the pattern of hydrogen bonds
and how the amino acid chain is folded.
Give a definition for
a hydrogen bond.
Nitrogen
The alpha helix is a rod-like
structure. The peptide main
chain forms the inner part of the
rod as shown in the figure on
the left (amino acid R-groups
are not shown for simplicity).
H-bond
Oxygen
The coil is held together by
hydrogen bonds between a
carbonyl oxygen and the
hydrogen attached to nitrogen
four residues ahead.
If you look down the helix from
the top, you can see it is like a
tube. The amino acid side chains
extend out from the rod, as
shown here.
In a β-sheet, the polypeptide
chain is almost fully extended to
form a β-strand. β-strands are
folded so that sections of the
chain lie alongside each other.
β-sheets are stabilised by
hydrogen bonding between
strands, in the same way as
shown previously for the αhelix.
Strands can run in the same
direction (parallel sheet) or the
opposite direction (anti-parallel
sheet).
H-bond
In 3D images of
proteins, β-sheets are
often represented by
long
flat
arrows,
pointing in the direction
the strand is running.
This makes it easy to
pick out parallel or antiparallel sheets.
β-turns are regular structures which allow the βstrands to reverse direction. Each β-turn is
made up of 4 amino acid residues. The C=O of
residue 1 hydrogen bonds with the N-H of
residue 3.
H-bond
β-turn
These 3D images
show how the βturn allows two βsheets to run in
opposite
directions. Notice
the shape of the
turn, which is
common in many
protein structures.
Produced by Lucy Jakubecz at Newcastle University as part of an MChem project.