Coiled Coils

1
Coiled Coils

• 7.88J Protein Folding
• Prof. David Gossard
• Room 3-336, x3-4465
• Gossard_at_mit.edu
• September 28, 2005

2
Outline

• Key Features of Coiled Coils
• A Particular Example
• GCN4 Leucine Zipper (2ZTA)

3
Fibrous protein examples

• Tropomyosin
• Intermediate
• filament protein
• Lamin
• M-protein
• Paramyosin
• Myosin

Cohen, C. and D.A.D. Perry, (1990) a-helical
coiled coils and bundles How to design an
a-helical protein, PROTEINS Structure,
Function, and Genetics 71-15.
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Other example GCN4

• Gene regulation in yeast
• Recognizes a specific DNA sequence
• a-helices sidechains contact major groove of
  DNA
• DNA-protein fit is specific and strong
• Protein dimerization and DNA binding functions
  are integrated

Alberts, et.al., (2002), Molecular Biology of the
Cell, 4th edition, Garland
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Coiled Coils

• Left-handed spiral of right-handed helices
• May be parallel
• or anti-parallel

N
C
N
C
C
N
N
C
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Equations of Helix (Coil)
ro - radius
Po - pitch
a pitch angle

• tan 1 (2pr0/p0)

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Equations of Coiled-Coil
z
x(t) r0 cos w0t r1cos w0t cos w1t - r1cos a
sin w0t sin w1t y(t) r0 sin w0t r1sin w0t cos
w1t r1cos a cos w0t sin w1t z(t) p0(w0t) -
r1sin a sin w1t
a tan 1 (2pr0/p0)
y
x
F.H.C. Crick, The Fourier Transform of a
Coiled-coil, Acta Cryst. (1953), 6, 685-689
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Questions

• What is the nature of the interaction between the
  coils?
• What is the angle of twist?
• What are the sequence determinants?

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Knobs in Holes Packing
Helix axis
F.H.C. Crick, The Packing of a-helices Simple
Coiled-coils, Acta Cryst. (1953), 6, 689-697
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Features of Coiled Coil

• Heptad repeat in sequence
• a b c d e f gn
• Hydrophobic residues at a and d
• Charged residues at e and g

/-
Hydrophobic residues at a and d
Charged residues at e and g
/-
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Significance of Heptad Repeat
Residues at d and a form hydrophobic core
Residues at e and g form ion pairs
/-
-/
-/
/-
Figure adapted from Cohen, et.al., PROTEINS
Structure, Function and Genetics 71-15 (1990)
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Heptad Repeat in 3D
Charged residues
/-
g
-/
/-
e
g
c
f
f
d
d
b
e
a
b
c
a
-/
Hydrophobic residues
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Hydrophobic Core is on Axis of Superhelix (
Straight)
d
a
d
a
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Charged Residues Provide Stability, Registration
Charged residues e and g
Ion pairs between coils
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Demonstration

• Heptad repeat in 3D
• Full Coiled Coil in 3D
• Knobs in Holes Packing

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GCN4-p1 Leucine Zipper (2ZTA)

• Parallel Coiled Coil
• (last) 31 residues 45 A
• 8 turns
• Separation of minor axes 9.3 A
• Major helix pitch 181 A/turn
• Major helix 90o

Erin OShea, Juli D. Klemm, Peter S. Kim, and Tom
Alber, X-ray Structure of the GCN4 Leucine
Zipper, a Two-Stranded, Parallel Coiled Coil,
Science, 254, pp. 539-544, October 25, 1991
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GCN4-p1 Leucine Zipper (2ZTA)

• Residues contain heptad repeat
• Ion pairs
• Lys15 Glu20
• Glu22 Lys27
• Glu22 Lys27

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Crossing Angle 18o
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3-Stranded Coiled Coil!? (parallel)

• Axial symmetry
• Hydrophobic core
• Ion pairs

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4-Stranded Coiled Coil!? (parallel)

• Axial symmetry
• Hydrophobic core
• Ion pairs

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3 4-Stranded Coiled Coils

• 3-stranded
• Gp17 (T7)
• Fibrinogen (heterotrimer)
• GCN4 mutant
• 4-stranded parallel
• GCN4 mutants
• 4-stranded anti-parallel
• Myohaemerythrin
• Tobacco mosaic virus
• Cytochrome c
• Apoferritin

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END