Protein Secondary Structure

1
Lecture 7

• Protein Secondary Structure

2
Peptide bond
3
Rotation is limited
?
?
?
?-
4
Proline a special case
Often found in cis peptide bond structures
Very constrained conformation
5
Ramachandran Plot
Defines allowed ? and ?
6
? Helix
? -60 º ? -45 to -50º

• Factors in stability
• Maximum H-bonding
• Rigidity of peptide bonds
• Side chain interactions
• Prolines
• Helix dipole

7
? Helix Views
Side chains are on outside of helix
8
Rules for helix formation
Hydrogen bond CO group in nth residue forms
hydrogen bond with NH group in (n4)th residue.
Determines polarity Handedness L-amino acids
only make right handed helices (Looking down
helix axisclockwise) Side chain
interactionsSide chains in the n and n3 or n4
positions can interact (either to stabilize or
destabilize the helix)
Prolines disrupt helices
Glycine may also disrupt helices
9
? Helix Dipole
10
Identifying patterns that form helices
Helices with one side exposed at the protein
surface
I
V
M
F
8
L
1
12
I
15
Helical wheel (4 turns of a helix)
5
M
4
16
I
9
C
11
Polar and nonpolar Sides Amphipathic helix
A
2
G
18
7
13
S
D
6
14
Q
17
R
3
10
T
S
D
11
? Pleated Sheet

• Interchain H-bonding
• Small amino acid side chains
• Parallel or antiparallel

Antiparallel
12
Antiparallel ? Sheet
13
Parallel ? Sheet
14
Silk Antiparallel ? Sheet
15
? Bend
16
Fibrous Proteins
Repeating units One type of 2º structure
Keratins hair, skin, nails Collagen cartilage,
skin, bone Elastin blood vessels Fibronectin clot
ting factors
17
Crosslinking is found in fibrous protein
Altering crosslinking in hair
18
Collagen helix
Not an a-helix! Repeat Gly-X-Pro X often is Hyp
19
Collagens Unusual Amino Acids
20
Superhelices are crosslinked
Collagens Unusual Amino Acids