Coiled Coils 7.88J Protein Folding Prof. David Gossard Room 3-336, x3-4465 [email protected] September...
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Transcript of Coiled Coils 7.88J Protein Folding Prof. David Gossard Room 3-336, x3-4465 [email protected] September...
![Page 1: Coiled Coils 7.88J Protein Folding Prof. David Gossard Room 3-336, x3-4465 Gossard@mit.edu September 28, 2005.](https://reader034.fdocuments.in/reader034/viewer/2022052509/56649cf05503460f949c0029/html5/thumbnails/1.jpg)
Coiled Coils
7.88J Protein Folding
Prof. David Gossard
Room 3-336, x3-4465
September 28, 2005
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Outline
• Key Features of Coiled Coils
• A Particular Example– GCN4 Leucine Zipper (2ZTA)
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Fibrous protein examples
• Tropomyosin
• Intermediate
filament protein
• Lamin
• M-protein
• Paramyosin
• Myosin
Cohen, C. and D.A.D. Perry, (1990) “-helical coiled coils and bundles: How to design an -helical protein”,PROTEINS: Structure, Function, and Genetics 7:1-15.
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Other example – GCN4
• Gene regulation in yeast• Recognizes a specific DNA
sequence– -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, 4 th edition, Garland
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Coiled Coils
• Left-handed spiral of right-handed helices
• May be parallel
or anti-parallel
NC
NN
N
C
C
C
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Equations of Helix (Coil)
o > 0 right-handed
= tan –1 (2r0/p0)x(t) = ro cos(o t)
y(t) = ro sin(o t)
z(t) = Po (o t /2)
ro - radius
Po - pitch
= pitch anglex y
R(t)
t
roPo
oz
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Equations of Coiled-Coil
x(t) = r0 cos 0t + r1cos 0t cos 1t - r1cos sin 0t sin 1ty(t) = r0 sin 0t + r1sin 0t cos 1t + r1cos cos 0t sin 1tz(t) = p0(0t) - r1sin sin 1t
F.H.C. Crick, “The Fourier Transform of a Coiled-coil”,Acta Cryst. (1953), 6, 685-689
= tan –1 (2r0/p0) x y
z
x y
z
t
p(t)
x'y'
z'
Major helix, radius ro ,
left-handed (o<0)
Minor helix, radius r1,
right-handed (1>0) t
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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
F.H.C. Crick, “The Packing of -helices: Simple Coiled-coils”,Acta Cryst. (1953), 6, 689-697
Helix axis
"about 20o ..."
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Features of Coiled Coil
• Heptad repeat in sequence– [a b c d e f g]n
• Hydrophobic residues at “a” and “d”
• Charged residues at “e” and “g”
Hydrophobic residues at “a” and “d”
Charged residues at “e” and “g”
ab
cd
e
f
g
+/-
+/-
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Significance of Heptad Repeat
Figure adapted from Cohen, et.al., PROTEINS: Structure, Function and Genetics 7:1-15 (1990)
ab
cd
e
f
g
ab
cd
e
f
g
Residues at “d” and “a”form hydrophobic core
Residues at “e” and “g”form ion pairs
+/-
+/-
-/+
-/+
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Heptad Repeat in 3D
a
b
c
d
ef g
ab
cd
e
f
g
Hydrophobic residues
Chargedresidues
+/-
-/+
+/- -/+
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Hydrophobic Core is on Axis of Superhelix ( ~Straight)
d
ad
a
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Charged Residues Provide Stability, Registration
Charged residues“e” and “g”
Ion pairsbetweencoils
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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 O’Shea, 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
a b c d e f gARG1 MET2 LYS3 GLN4 LEU5 GLU6 ASP7 LYS8
VAL9 GLU10 GLU11 LEU12 LEU13 SER14 LYS15ASN16 TYR17 HIS18 LEU19 GLU20 ASN21 GLU22VAL23 ALA24 ARG25 LEU26 LYS27 LYS28 LEU29VAL30 GLY31
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Crossing Angle ~18o
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3-Stranded Coiled Coil!? (parallel)
ab
cd
e
f
g a
b
c
d
f
g
a
b
c
d e
f
g
e
• Axial symmetry
• Hydrophobic core
• Ion pairs
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4-Stranded Coiled Coil!? (parallel)
ab
cd
e
f
g
ab
cd
e
f
g
a
b c
d
e
f
g
a
bc
d
e
f
g
• 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