Coiled Coils
7.88J Protein Folding
Prof. David Gossard
Room 3-336, x3-4465
Gossard@mit.edu
September 28, 2005
Outline
• Key Features of Coiled Coils
• A Particular Example
– GCN4 Leucine Zipper
(2ZTA)
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 7:1-15.
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, 4 th edition, Garland
Coiled Coils
• Left-handed spiral of right-handed helices
• May be parallel
N
N
C
C
or anti-parallel
C
N
N
C
Equations of Helix (Coil)
z
o t
ro - radius
Po
x
R(t)
ro
a
x(t) = ro cos(o t)
y(t) = ro sin(o t)
z(t) = Po (o t /2p)
y
o > 0 right-handed
Po - pitch
a = pitch angle
= tan –1 (2pr0/p0)
Equations of Coiled-Coil
z
z
Minor helix, radius r1,
right-handed (1>0)
z'
t
p(t)
x'
Major helix, radius ro ,
left-handed (o<0)
y'
x
t
y
x(t) = r0 cos 0t + r1cos 0t cos 1t - r1cos a sin 0t sin 1t
y(t) = r0 sin 0t + r1sin 0t cos 1t + r1cos a cos 0t sin 1t
z(t) = p0(0t) - r1sin a sin 1t
a = tan –1 (2pr0/p0)
x
F.H.C. Crick, “The Fourier Transform of a Coiled-coil”,
Acta Cryst. (1953), 6, 685-689
y
Questions
• What is the nature of the
interaction between the coils?
• What is the angle of twist?
• What are the sequence
determinants?
“Knobs in Holes” Packing
"about 20o ..."
Helix axis
F.H.C. Crick, “The Packing of a-helices: Simple Coiled-coils”,
Acta Cryst. (1953), 6, 689-697
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”
+/b
e
a
f
Hydrophobic residues
at “a” and “d”
d
c
g
+/-
Charged residues at “e” and “g”
Significance of Heptad Repeat
Residues at “d” and “a”
form hydrophobic core
Residues at “e” and “g”
form ion pairs
-/+
b
g
e
a
+/-
c
d
f
f
d
c
g
+/-
a
e
b
-/+
Figure adapted from Cohen, et.al., PROTEINS: Structure, Function and Genetics 7:1-15 (1990)
Heptad Repeat in 3D
Charged
residues
+/g
-/+
+/-
g
f
e
c
d
d
b
e
a
c
f
a
Hydrophobic residues
-/+
b
Hydrophobic Core is on Axis of
Superhelix ( ~Straight)
d
d
a
a
Charged Residues Provide Stability, Registration
Charged residues
“e” and “g”
Ion pairs
between
coils
Demonstration
• Heptad repeat in 3D
• Full Coiled Coil in 3D
• “Knobs in Holes” Packing
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
GCN4-p1 Leucine Zipper
(2ZTA)
• Residues contain heptad repeat
ARG1
a
MET2
VAL9
ASN16
VAL23
VAL30
b
LYS3
GLU10
TYR17
ALA24
GLY31
c
GLN4
GLU11
HIS18
ARG25
• Ion pairs
– Lys15 – Glu20’
– Glu22 – Lys27’
– Glu22’ – Lys27
d
LEU5
LEU12
LEU19
LEU26
e
GLU6
LEU13
GLU20
LYS27
f
ASP7
SER14
ASN21
LYS28
g
LYS8
LYS15
GLU22
LEU29
Crossing Angle
o
~18
3-Stranded Coiled Coil!?
(parallel)
• Axial symmetry
• Hydrophobic core
• Ion pairs
b
c
f
g
e
b
d
e
a
a
d
d
f
c
g
g
a
c
e
b
f
4-Stranded Coiled Coil!?
(parallel) f
• Axial symmetry
• Hydrophobic core
• Ion pairs
b
c
b
g
e
a
d
e
g
a
c
d
f
f
a
d
c
g
a
e
d
e
g
c
b
f
b
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
END