the α-helix forms within a continuous strech of the polypeptide chain 5.4 Å rise, 3.6 aa/turn 1.5...
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![Page 1: The α-helix forms within a continuous strech of the polypeptide chain 5.4 Å rise, 3.6 aa/turn 1.5 Å/aa N-term C-term prototypical = -57 ψ = -47](https://reader035.vdocuments.pub/reader035/viewer/2022070400/56649f125503460f94c252a3/html5/thumbnails/1.jpg)
The α-helix forms within a continuous strech of the polypeptide chain
5.4 Å rise,3.6 aa/turn
1.5 Å/aa
N-term
C-term
prototypical = -57ψ = -47
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α-Helices have a dipole moment, due to unbonded and aligned N-H and C=O groups
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β-Sheets contain extended (β-strand) segments from separate regions of a protein
(6.5Å repeat length in parallel sheet)
prototypical = -119, ψ = +113
prototypical = -139, ψ = +135
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Figure 6-13
Antiparallel β-sheets may be formed by closer regions of sequence than parallel
Beta turn
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The stability of helices and sheets depends on their sequence of amino acids
• Intrinsic propensity of an amino acid to adopt a helical or extended (strand) conformation
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The stability of helices and sheets depends on their sequence of amino acids
• Intrinsic propensity of an amino acid to adopt a helical or extended (strand) conformation
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The stability of helices and sheets depends on their sequence of amino acids
• Intrinsic propensity of an amino acid to adopt a helical or extended (strand) conformation
• Interactions between adjacent R-groups– Ionic attraction or repulsion– Steric hindrance of adjacent bulky groups
Helix wheel
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The stability of helices and sheets depends on their sequence of amino acids
• Intrinsic propensity of an amino acid to adopt a helical or extended (strand) conformation
• Interactions between adjacent R-groups– Ionic attraction or repulsion– Steric hindrance of adjacent bulky groups
• Occurrence of proline and glycine• Interactions between ends of helix and aa R-groups
N-term
d+
C-term
d-
His
Lys
Arg
Glu
Asp
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Turns are important secondary structures that change the direction of the chain
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Backbones are usually trans at the peptide bond, but cis-Pro is found in some β-turns
C N
HO
C N+
H-O
C N
O
H
C N+
-O
H
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Tertiary structure combines regular secondary structures and loops
Bovine carboxypeptidase A
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Most dihedral angles of a protein’s tertiary structure are “allowed”
Structure:pyruvate kinase
Note: glycine not shown
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Fibrous proteins are dominated by secondary (and quaternary) structure
Silk fibroin forms stacked, antiparallel β-sheets
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Figure 6-15b
Fibrous proteins are dominated by secondary (and quaternary) structure
α-Keratin forms an α-helical coiled-coil
Collagen forms a triple-helix
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Regular spacing of hydrophobic aa’s in α-keratin promotes quaternary interactions
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Figure 6-18
Gly-X-Y motif and hydroxylated aa’s of collagen allow for tight coiling and packing
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Globular proteins are compact and often combine multiple secondary structures
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Globular proteins have hydrophobic groups inside and hydrophilic groups on the surface
Horse heart cytochrome C
aa side chains: green=hydrophilic; orange=hydrophobic
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Hydropathic index can be plotted for a protein, to predict internal & external zones
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Particular arrangements of polar and apolar residues can form amphipathic helices
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An alternating sequence of polar and apolar residues can form an amphipathic sheet
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Figure 6-28
Some tertiary structures contain common patterns, or motifs, of secondary structures (= supersecondary structures)
βαβ β-hairpins αα(coiled-coil)
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Proteins folds can be grouped by predominant secondary structure(s)
α β α/β