Lecture 10: Protein structure

– 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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2 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

Structural properties predicted by Ramachandran Diagram

Table 8-1 van der Waals Distances for Interatomic Contacts.

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Figure 8-8Conformation angles in proteins.

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H

C H

COO-

H3N+

R

C H

COO-

H3N+

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.

Figure 8-10 Examples of helices.

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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.

Figure 8-11 The right-handed 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.

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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.

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.

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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)

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.

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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.

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.

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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.

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.

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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

Figure 8-22 Reverse turns in polypeptide chains.

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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.

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

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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

Figure 8-25 The microscopic organization of hair.

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Figure 8-26 The structure of keratin.

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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.

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.

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