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Motives of secondary structures
Consecutive elements of secondary structure can
assemble together and form recurring or frequently
found structures in protein folds (tertiary structure).
These special assemblies are called motives and
represent supra-secondary elements, often associated
with special structural or functional properties.
In a motif, a helices and/or b strands are linked together
by loops of variable lengths; the main chain of the latter
is devoid of regular structure.
The atom density in an assembled motif is generally
higher than that before the assembly.
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The helix-turn-helix motif
Two a helices that are connected by a short loop region in a
specific geometric arrangement.
Two such motifs are shown: (a) the DNA-binding motif and (b)
the calcium-binding motif which is present in many proteins
whose function is regulated by calcium
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The DNA binding motif
a
c
b
d
a. Cro molecules from bacteriophage lambda form dimers
both in solution and in the crystal structure.
b. The DNA-binding helix-turn-helix motif in lambda Cro.
c. The helix-turn-helix motif sitting in the major groove of
DNA.
d. A schematic space-filling model of the dimer of Cro
bound to a bent B-DNA molecule.
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EcoRV binding and restriction
5’-XXXGAT ATCXXX-3’
3’-XXXCTA TAGXXX-5’
Schematic representation of the proposed DNA-sequence
recognition mechanism by EcoRV in which only the most
important differences between the states are shown. First,
EcoRV in an open state binds to a random DNA sequence and
forms a loosely bound open complex (step 1). Then, upon
recognition of the outer base pairs, GAxxTC, a partially bound
closed complex with bent DNA is formed (step 2). Finally,
recognition of the center base pairs, xx = TA, results in a tightly
bound cleavage-ready complex, with a full kink of 50° (step 3).
The distance between the “arms” of the protein, E, decreases
from step 1 to step3 (E0 < E1 < E2 < E 3). Simultaneously, the
distance between the protein and the DNA, D, becomes smaller
(D0 < D1 < D2 < D3). From Zahran et al, JMB 2010.
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The Ca-binding motif
(a) The calcium-binding motif is symbolized by a right hand. Helix E (red) runs from
the tip to the base of the forefinger. The flexed middle finger corresponds to the
green loop region of 12 residues that binds calcium (pink). Helix F (blue) runs to
the end of the thumb. (b) The calcium atom is bound to one of the motifs in the
muscle protein troponin-C through six oxygen atoms: 5 from the side chains of Asp
and Glu; and one from the main chain. In addition, a water molecule (W) is bound to
the calcium atom. (c) Schematic diagram illustrating that the structure of troponin-C
is built up from four EF motifs---colored as in (a). Two of these bind Ca.
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Antiparallel beta hair pin
Adjacent antiparallel b strands are joined by hairpin loops.
Such loops are frequently short and do not have regular secondary structure. Nevertheless,
many loop regions in different proteins have similar structures. (a) Histogram showing the
frequency of hairpin loops of different lengths in 62 different proteins. (b) The two most
frequently occurring two-residue hairpin loops; Type I turn to the left and Type II turn to the right.
Bonds within the hairpin loop are green. [(a) Adapted from B.L. Sibanda and J.M. Thornton,
Nature 316: 170-174, 1985.]
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The beta hair-pin
The hairpin motif is very frequent in b sheets and is built up
from two adjacent antiparallel b strands that are joined by a loop region.
Two examples of such motifs are shown. (a) Schematic diagram of the structure of
bovine trypsin inhibitor. The hairpin motif is colored red. (b) Schematic diagram of
the structure of the snake venom erabutoxin. The two hairpin motifs within the b
sheet are colored red and green. (Adapted from J. Richardson.)
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Possible arrangements of two consecutive b hair pins
Two sequentially adjacent hairpin motifs
can be arranged in 24 different ways
into a b sheet of four strands.
(a) Topology diagrams for those
arrangements that were found in a survey
of all known structures in 1991. The Greek
key motifs in (i) and (v) occurred 74 times,
whereas the arrangement shown in (viii)
occurred only once. (b) Topology diagrams
for those 16 arrangements that did not
occur in any structure known at that time.
Most of these arrangements contain a pair
of adjacent parallel b strands.
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The Greek key
a. The Greek key motif is found in antiparallel b sheets when four adjacent b
strands are arranged in the pattern shown as a topology diagram.
b. The motif occurs in many b sheets and is exemplified here by the enzyme
Staphylococcus nuclease. The four b strands that form this motif are colored
red and blue.
c. Suggested folding pathway from a hairpin like structure to the Greek
key motif.
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The b-a-b motif
Two adjacent parallel b strands are usually connected by an a helix
from the C-terminus of strand 1 to the N-terminus of strand 2.
Most protein structures that contain parallel b sheets are built up
from combinations of such b-a-b motifs (right-handed structures).
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From motifs to domains
Motifs that are adjacent
in the amino acid
sequence are also
usually adjacent in the
three-dimensional
structure.
Triose-phosphate
isomerase is built up from
four b-a-b-a motifs that
are consecutive both in
the amino acid sequence
(a) and in the threedimensional structure (b).
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The Felix fold
Four-helix bundles often occur as domains in a proteins.
The arrangement of the a helices is such that adjacent
helices in the amino acid sequence are also adjacent in the 3-D
structure. Some side chains from all four helices are buried in the middle of the bundle, where they form a
hydrophobic core. (a) Representation of the path of the polypeptide chain in a four-helix-bundle domain.
Red cylinders are a helices. (b) View of a projection down the bundle axis. Large circles represent the
main chain of the a helices; small circles are side chains. Green circles are the buried hydrophobic side
chains; red circles are mainly hydrophilic side chains exposed on the surface of the bundle.
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Felix structures
The polypeptide
chains of cytochrome
b562 and human
growth hormone both
form four-helixbundle structures.
In cytochrome b562 (a)
adjacent helices are
antiparallel, whereas
the human growth
hormone (b) has two
pairs of parallel a
helices joined in an
antiparallel fashion.
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Felix structures
Schematic
diagram of the
dimeric Rop
molecule.
Each subunit
comprises two
a helices
arranged in a
coiled-coil
structure with
side chains
packed into the
hydrophobic
core according
to the "knobs in
holes" model.
The two
subunits are
arranged in
such a way that
a bundle of four
a helices is
formed.
Schematic diagram of the structure of one
domain of a bacterial muramidase.
The structure is built up from 27 a helices (450 aa)
arranged in a two-layered ring. The ring has a
large central hole, like a doughnut, with a diameter
of about 30 angstrom.
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The globin fold
Schematic
diagram of the
globin domain.
The eight alpha
helices are
labeled A-H. A-D
are red, E and F
green, and G and
H blue. The heme
group is shown in
white. (Adapted
from originals
provided by A.
Lesk.) ca-Prot_Enz 15
Ridges and grooves – topography of a helices
The side chains on the
surface of an a helix form
ridges separated by
grooves.
(a) An a helix with each
residue represented by the
first atom in the side chain,
Cb. (b) The surface relief of
a polyalanine a helix in the
orientation shown in (a).
Sections are cut through a
space-filling model and
superimposed. The residue
numbers are placed on the
side-chain atom. The ridges
caused by the side chains
separated by four residues
are shown as lines. (c) The
same as (b), but here the
ridges are caused by side
chains separated by three
residues
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The topography of packing
Fitting the ridges
from one helix into
the grooves of the
other helix results
in tight packing.
(a) Two a helices, I
and II, with ridges
from side chains
separated by four
residues. Panels 1
and 2 are the same
view of the two a
helices. In panel 3 the
blue helix is turned
over through 180o to
form an interface with
the red helix. In panel
4 the orientation of
the helices has been
rotated 50o to pack
the ridges of one
helix into the grooves
of the other.
(b) In the red helix the ridges are formed by side chains separated by four residues and in
the blue a helix by three residues. The helices are rotated 20o in order to pack ridges into
grooves, in a direction opposite that in (a). (Adapted from C. Chothia et al., Proc. Natl. Acad.
Sci. USA 74: 4130-4134, 1977).
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Hemoglobin: a heterotetramer
The hemoglobin
molecule is built up of
four polypeptide
chains: two a chains
and two b chains.
Each chain has a threedimensional structure
similar to that of
myoglobin: the globin
fold. In sickle-cell
hemoglobin Glu 6 in the b
chain is mutated to Val,
thereby creating a
hydrophobic patch on the
surface of the molecule.
The structure of
hemoglobin
was
determined in 1968 to 2.8
A resolution in the lab of
Max Perutz at the MRC
Laboratory of Molecular
Biology, Cambridge, UK.
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Fibroid polymerization in sickle-cell hemoglobin
Electron
micrographs of
sickle-cell
hemoglobin
fibers are
shown in crosssection in (b)
and along the
fibers in (c). [(b)
and (c) from J.T.
Finch et al., Proc.
Natl. Acad. Sci.
USA 70: 718-722,
1973.]
Sickle-cell hemoglobin molecules polymerize due to the hydrophobic patch introduced by
the mutation Glu 6 to Val in the b chain.
The diagram (a) illustrates how this hydrophobic patch (green) interacts with a hydrophobic
pocket (red) in a second hemoglobin molecule, whose hydrophobic patch interacts with the
pocket in a third molecule, and so on (inset).
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The a helix coiled-coil structure
Schematic diagram of the coiled-coil structure.
Two a helices are intertwined and gradually coil around each
other.
Repetitive pattern of amino acids in a coiled-coil a
helix.
(a) The amino acid sequence of the transcription factor
GCN4 showing a heptad repeat of leucine residues.
Within each heptad the amino acids are labeled a-g.
(b) Schematic diagram of one heptad repeat in a coiled-coil structure showing the
backbone of the polypeptide chain. The a helices in the coiled-coil are slightly distorted
so that the helical repeat is 3.5 residues rather than 3.6, as in a regular helix. There is
therefore an integral repeat of seven residues along the helix.
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Stabilizing interactions in coiled-coil fold
Packing of hydrophobic side chains between the two a helices in a coiled-coil structure.
Every 7th residue in both helices is a leucine, labeled "d." Due to the heptad repeat, the d-residues
pack against each other along the coiled-coil. Residues labeled "a" are also usually hydrophobic
and participate in forming the hydrophobic core along the coiled-coil.
Salt bridges can stabilize coiled-coil structures in heterodimeric coiled-coil structures.
The residues labeled "e" and "g" in the heptad sequence are close to the hydrophobic core and can
form salt bridges between the two a helices of a coiled-coil structure, the e-residue in one helix with
the g-residue in the second and vice versa. (a) Schematic view from the top of a heptad repeat. (b)
Schematic view from the side of a coiled-coil structure.
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Knobs in holes packing
Packing side chains in the hydrophobic core of coiled-coil structures according to the
"knobs in holes" model.
The positions of the side chains along the surface of the cylindrical a helix is projected onto a
plane parallel with the helical axis for both a helices of the coiled-coil. (a), (b) Projected
positions of side chains in helices 1 and 2.
(c) Superposition of (a) and (b) using the relative orientation of the helices in the coiled-coil
structure. The side-chain positions of the first helix, the "knobs," superimpose between the
side-chain positions in the second helix, the "holes." The green shading outlines a d-residue
(leucine) from helix 1 surrounded by four side chains from helix 2, and the brown shading
outlines an a-residue (usually hydrophobic) from helix 1 surrounded by four side chains from
helix 2.
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