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) “-helical coiled coils and bundles: How to design an -helical protein”,PROTEINS: Structure, Function, and Genetics 7:1-15.

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

Coiled Coils

• Left-handed spiral of right-handed helices

• May be parallel

or anti-parallel

NC

NN

N

C

C

C

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

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

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

F.H.C. Crick, “The Packing of -helices: Simple Coiled-coils”,Acta Cryst. (1953), 6, 689-697

Helix axis

"about 20o ..."

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

+/-

+/-

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

+/-

+/-

-/+

-/+

Heptad Repeat in 3D

a

b

c

d

ef g

ab

cd

e

f

g

Hydrophobic residues

Chargedresidues

+/-

-/+

+/- -/+

Hydrophobic Core is on Axis of Superhelix ( ~Straight)

d

ad

a

Charged Residues Provide Stability, Registration

Charged residues“e” and “g”

Ion pairsbetweencoils

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

• 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

Crossing Angle ~18o

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

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

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