Transcript Parallel pleated sheet

Lecture 10: Protein structure
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Protein structure
Alpha helix
Beta sheet
Turns or bends
Ramachandran Diagrams
• Show the allowed conformations of polypeptides.
• These work, because the sterically allowed values of 
and  can be determined by calculating the distances
between the atoms at all values  and  for the central
peptide unit.
• Sterically forbidden conformations are those in which
any nonbonding interatomic distance is less than its
corresponding van der Waals distance.
• This info can be summarized by the Ramachandran
Diagram or Conformation map
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Structural properties predicted by
Ramachandran Diagram
Regions of “normally allowed” torsion
angles are shown in blue.
Green regions are the “outer limit”
regions.
Secondary structure
 (deg)
 (deg)
Right handed  helix ()
-57
-47
Parallel  pleated sheet ()
-119
113
Antiparallel  pleated sheet ()
-139
135
Right-handed 310 helix (3)
-49
-26
Right-handed helix ()
-57
-70
2.27 ribbon (2)
-78
59
Left-handed polyglycine II and
poly-L-proline II helices (II)
-79
150
Collagen (C)
-51
151
Left-handed  helix (L)
57
47
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Table 8-1 van der Waals Distances for
Interatomic Contacts.
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Figure 8-8 Conformation
angles in proteins.
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+
H3N
COOC
R
H
+
H3N
COO-
C
H
H
Secondary structure
• 3 main types of secondary structure
– Alpha helix
– Beta-sheet
– Turns or bends
Helical structures
• A helix may be characterized by the number, n, of
peptide units per helical turn and by its pitch, p, the
distance the helix rises along its axis per turn.
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Figure 8-10 Examples of
helices.
d=p/n
Helical structures
• A helix may be characterized by the number, n, of peptide units per
helical turn and by its pitch, p, the distance the helix rises along its
axis per turn.
  helix - the only helical polypeptide conformation that has allowed
conformation angles and a favorable hydrogen bonding pattern.
Always right-handed for L- amino acids (torsion angles 
, n = 3.6 residues per turn and the pitch is 5.4 Å. (D-
amino acids is opposite.
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Figure 8-11 The righthanded  helix.
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Figure 8-12
Stereo, space-filling representation of an  helical
segment of sperm whale myoglobin (its E. helix) as determined by
X-ray crystal structure analysis.
Helical structures
• Helices are formed by hydrogen bonding and
are described by the notation nm
– n = number of residue per helical turn
– m = number of atoms, including H, in the
ring that is closed by the hydrogen bond.
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Figure 8-13
The hydrogen bonding
pattern of several polypeptide helices.
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Figure 8-14 Comparison of the two polypeptide helices
that occasionally occur in proteins with the commonly
occurring  helix.
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Figure 8-15
The polyproline II helix.
Beta structures
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As with the  helix the  pleated sheet has repeating  and angles that fall in the
allowed region of the Ramachandran diagram
In  pleated sheets hydrogen bonding occurs between neighboring polypeptide
chains.
Two main forms of  pleated sheets
Antiparallel  pleated sheet in which the sheets in which the neighboring hydrogen
bonded polypeptide chains run in opposite directions.
Parallel  pleated sheet in which the hydrogen bonded chains extend in the same
direction.
The conformations in which these  structures are optimally hydrogen bonded vary
somewhat from that of a fully extended polypeptide so that they have a rippled or
pleated edge on appearance.
Common structural motifs (from 2 to 22 polypeptide strands, average 6).
Polypeptide chains in a  sheet are up to 15 residues (avg. 6 with a length of 21 Å)
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Figure 8-16a  pleated sheets. (a) The
antiparallel  pleated sheets.
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Figure 8-16b  pleated sheets. (b) The
parallel  pleated sheets.
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Figure 8-17
A two-stranded  antiparallel
pleated sheet drawn to emphasize its
pleated appearance.
Beta structures
Parallel  pleated sheet less than 5 strands are rare.
– parallel  pleated sheet are less stable than antiparallel  pleated
sheet .
• Mixed parrallel-antiparallel  pleated sheet are common but only 20% of
the strandes in  pleated sheet have parallel bonding on one side and
antiparallel on the other side.
  pleated sheets in globular proteins have a right-handed twist, often
forming the central core of the protein.
• This right-handed twist arises from non-bonded interactions of L-a-amino
acids in the extended polypeptide chains.
• Topology (connectivity) of the polypeptide strands in a  pleated sheet
describes the connecting links of these assemblies which often consist of
long runs of polypeptide chain which usually contain helices.
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Figure 8-19a
Polypeptide chain folding in proteins illustrating
the right-handed twist of  sheets. (a) Bovine carboxypeptidase A.
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Figure 8-19b
Polypeptide chain folding in proteins illustrating
the right-handed twist of  sheets. (b) Chicken muscle triose
phosphate isomerase.
Beta structures
• Link that connects antiparallel strands is a simple hairpin
turn.
• For tandem parallel strands, linked by a crossover
connection that is out of the plane of the -sheet and
almost always have a right-handed helical sense.
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Figure 8-20
Connections between
adjacent polypeptide strands in  pleated
sheets.
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Figure 8-21
Origin of a right-handed
crossover connection.
Coil and loop conformations
• 50% of regular secondary structure is helices and  pleated sheets,
the other segments are coil or loop conformations. These have
structure (e.g. not random coils)
• Globular proteins consist of largely straight runs of 2 structure joined
by stretches of polypeptide that abruptly change direction (reverse
turns or  bends).
• Usually connect strands of antiparallel  sheets.
• Almost always occur on surface of the protein.
• Involve 4 successive amino acid residues arranged in one of two
ways
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Figure 8-22
Reverse turns in polypeptide
chains.
Coil and loop conformations
• Almost all proteins >60 residues have one or more loops
– Each loop is 6-16 residues that are not components of  sheets or
helices called  loops.
– Look like the Greek letter 
• Almost always located on the protein surface
• Involved in recognition.
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Figure 8-23
Space-filling representation of an Ω loop
comprising residues 40 to 54 of cytochrome c.
Fibrous Proteins
• Highly elongated molecules whose secondary structures
are their dominant structural motifs.
• Skin, tendon, bone-protective, connective, or supportive
roles; muscle proteins- motile functions.
• Structurally simple compared to globular proteins
• Rarely crystallize but x-ray diffractions can be done on
the fibers.
• Examples include keratin and collagen
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Figure 8-25
The microscopic
organization of hair.
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Figure 8-26 The structure of
 keratin.
Keratin
• Conformation of the coiled coil is from primary structure.
• Central 310 residue segment of each polypeptide has a
heptad (7-residue) pseudorepeat, a-b-c-d-e-f-g, with
nonpolar residues at positions a and d.
• Helix has 3.6 residues per turn, the a and d residues line
up on one side of the helix to form a hydrophobic strip
that interacts with a similar strip on another helix.
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Figure 8-27a
The two-stranded coiled coil.
(a) View down the coil axis showing the
interactions between the nonpolar edges of the
 helices.
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Figure 8-27b
The two-stranded coiled coil.
(b) Side view in which the polypeptide back
bone is represented by skeletal (left) and
space-filling (right) forms.