1. Lecture 10: Protein structure
Alpha helix
Beta sheet
Turns or bends

2. 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

3. Structural properties predicted by Ramachandran Diagram
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 ()
-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
Regions of “normally allowed” torsion angles are shown in blue.
Green regions are the “outer limit” regions.
This shows the sterically allowed phi psi angles for poly L alanine and wsa used to calculate the distances in table 8-1 Indicates that 75% of the Ramchandran diagram is inaccessible to a polypeptide chain. Allowed conformations depend on the van der Waals radii.
Only 3 small regions of the conformational map are phyically accessible to a polypeptide chains,
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4. Table 8-1 van der Waals Distances for Interatomic Contacts.
The distance allowed between different atoms as predicted by the Ramachandran chart.
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5. Figure 8-8 Conformation angles in proteins.
Experimental evidence supporting the Ramachandran chart.
This is the conformation angle distribution of all residues but Gly and Pro from 12 high resolution x-ray structures (blue dots) superimposed.
Why is glycine excluded?
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6. Gly has no beta carbon atom so it is much less sterically hindered than other amino acid residues.
Gly often is where the polypeptide backbone makes a sharp turn since it is not sterically hindered. R C H
COO-
H3N + H C
COO-
H3N +
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7. Secondary structure 3 main types of secondary structure Alpha helix
Beta-sheet
Turns or bends

8. 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.

9. Figure 8-10 Examples of helices.
Defiitions of helical pitch the number of repeating units per turn and the helical rise per prepeating unit.
Right handed helices have positive values
Left handed helices have negative values.
If n = 2 the helix turns into a nonchiral ribbon.
If p = 0 the helix becomes a closed ring.
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d=p/n

10. 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.

11. Figure 8-11 The right-handed a helix.
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12. Figure 8-12 Stereo, space-filling representation of an a helical segment of sperm whale myoglobin (its E. helix) as determined by X-ray crystal structure analysis.
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13. 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.

14. Figure 8-13 The hydrogen bonding pattern of several polypeptide helices.
In the cases shown the polypeptide chain is helically wound such that the N-H group on residue n forms a hydrogen bond with the C=O groups on residues n-2, n-3, n-4, or n-5
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15. Figure 8-14 Comparison of the two polypeptide helices that occasionally occur in proteins with the commonly occurring a helix.
Comparison of the two polypeptide helices that occasionally occur in proteins with the commonly occursing alpha helix.
The 310 helix which has 3.0 peptide units per turn and a pitch of 6 A, making it thinner and more elongaterd than that alpha helix
The alpha helix which has 3.6 peptide units per turn and a pitch 5.4 A
The pi helix wich has 4.4 peptide units per turn and a 5.2 A making wider shorter than the alpha helix . The peptide planes are indicated.
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16. Figure 8-15 The polyproline II helix.
Polyglycine forms a nearly identical helix (polyglycine II).
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17. Beta structures
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)

18. Figure 8-16a b pleated sheets. (a) The antiparallel b pleated sheets.
Hydrogen bonds are indicated by dashed lines and side chains are omitted for clarity.
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19. Figure 8-16b b pleated sheets. (b) The parallel b pleated sheets.
The conformation in which these beta structures are optimally hydrogen bonded for a fully extended polypeptide (phi psi 180). They therefore have ripled or pleated edge-on appearance, which accounts for the appellation pleated sheet.
B-sheets are
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20. Figure 8-17 A two-stranded b antiparallel pleated sheet drawn to emphasize its pleated appearance.
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21. 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.

22. Figure 8-19a Polypeptide chain folding in proteins illustrating the right-handed twist of b sheets. (a) Bovine carboxypeptidase A.
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23. Figure 8-19b Polypeptide chain folding in proteins illustrating the right-handed twist of b sheets. (b) Chicken muscle triose phosphate isomerase.
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24. 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.

25. Figure 8-20 Connections between adjacent polypeptide strands in b pleated sheets.
Simple hairpin connection between beta sheets.
a right handed crossover between successive strands of parallel beta sheets
a left handed crossover connection between parallel beta sheets.
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26. Figure 8-21 Origin of a right-handed crossover connection.
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27. 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

28. Figure 8-22 Reverse turns in polypeptide chains.
Type I and type II bends differ by a 180 flip of the peptide unit linking residues 2 and 3. Both bends contain a hydrogen bond although deviations from these ideal conformations often disrupt this hydrogen bond.
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29. 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.

30. Figure 8-23 Space-filling representation of an Ω loop comprising residues 40 to 54 of cytochrome c.
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31. 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

32. Figure 8-25 The microscopic organization of hair.
A typical hair is composed mostly of alpha keratin macrofibrils (2000 A in diamter) constructed of microfibrils (80A in diamter). Cemented togetherr with an amorphous protein with high sulfur content..
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33. Figure 8-26 The structure of a keratin.
Alpha keratin polypeptides form closely associated pairs of alpha helices in which each pair is composed of a type I and type II keratin chain twisted in parallel into a left handed coil. The normal 5.4 A repeat distance of each alpha helix is slightly tilted yielding a 5.1 A spacing. This is called coiled coil structure.
Alpha keratin are composed of 310 residues of one polypeptide chain of ttypes I and II keratins in a dimeric coiled coil. The conformations of the polypeptides golublar N and C terminal domains are unknown.
Protofiliaments are formed from two staggered and antiparallel rows of associated head to tail cioled coils.
The protofilaments dimerize to forma protofibril, four of which form a microfibril.
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34. 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.

35. Figure 8-27a. The two-stranded coiled coil
Figure 8-27a The two-stranded coiled coil. (a) View down the coil axis showing the interactions between the nonpolar edges of the a helices.
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36. Figure 8-27b. The two-stranded coiled coil
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.
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