Coils
7.88J Coiled Protein Folding
Prof. David Gossard September 24, 2003
PDB Acknowledgements
The Protein Data Bank (PDB - http://www.pdb.org/) is the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data.
Berman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H.Weissig, I. N.Shindyalov, and P. E.Bourne. "The Protein Data Bank." Nucleic Acids Research 28 (2000): 235-242. (PDB Advisory Notice on using materials available in the archive: http://www.rcsb.org/pdb/advisory.html)
PDB molecules and citations used in the "Coiled Coils" Lecture Notes for 7.88J - Protein Folding
PDB ID: 2ZTA JRNL reference: O'Shea, E. K., J. K. Klemm, P. S. Kim., and T. Alber. "X-ray structure of the GCN4 leucine zipper, a twostranded, parallel coiled coil." Science 254 (1991): 539. Pages: 3 ("Outline"), 14-15 ("GCN4 Leucine Zipper")
Outline
Review Key Features of Coiled Coils
Examine a Particular Example
GCN4 Leucine Zipper (2ZTA)
Coiled Coils
Left-handed spiral of right-handed helices
May be parallel
N N C C
or anti-parallel
C N N C
2-Stranded Coiled Coils
GCN4 Tropomyosin Intermediate filament protein Lamin M-protein Paramyosin Myosin
Crick's Models
Geometry of Helix (Coil)
z Zot
Zo > 0 right-handed
P x ro y x(t) = ro cos(Zo t)
y(t) = ro sin(Zo t)
z(t) = P (Zo t /2S) R(t)
Geometry of Coiled-Coil
Minor
z helix t r1 ro x Major helix
t y
z'
y' x'
z
Zo < 0 Major axis left-handed Minor axis Z1 > 0 right-handed
x(t) = r0 cos Z0t + r1cos Z0t cos Z1t - r1cos D sin Z0t sin Z1t y(t) = r0 sin Z0t + r1sin Z0t cos Z1t + r1cos D cos Z0t sin Z1t z(t) = p0(Z0t) - r1sin D sin Z1t D = tan 1 (2Sr0/p0)
x
Crick, F. H. C. "The Fourier Transform of a Coiled-coil." Acta Cryst. 6 (1953): 685-689.
y
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"
g +/Hydrophobic residues at "a" and "d" d f a e -/+ b c Charged residues at "e" and "g"
Figure adapted from Cohen, et.al., PROTEINS: Structure, Function and Genetics 7:1-15 (1990)
Significance of Heptad Repeat
Hydrophobic residues at "a" and "d"
form hydrophobic core with other coil
Charged residues at "e" and "g"
form ion pairs with oppositely charged residues on other coil may distinguish parallel from anti-parallel coiled coils
b f
e a d
+ g c f d a - e
c
b
g +
Figure adapted from Cohen, et.al., PROTEINS: Structure, Function and Genetics 7:1-15 (1990)
Heptad Repeat in 3D
+/ g +/ f b a c a g -/+ e d d e -/+ b c f Charged residues
Hydrophobic Core residues
Hydrophobic is on Axis of
Superhelix ( ~Straight)
d d a
a
Charged Residues Provide Stability, Registration
Charged residues "e" and "g"
Ion pairs between coils
"Knobs in Holes" Packing
"about 20..." Helix axis
Figure adapted from Crick, F. H. C. "The Packing of D-helices: Simple Coiledcoils." Acta Cryst. 6 (1953): 689-697.
GCN4 Leucine Zipper (2ZTA)
Parallel Coiled Coil Major helix pitch ~ 180 A/turn
8 turns 31 residues
O'Shea, Erin, 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 (October 25, 1991): 539-544.
GCN4 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 d LEU5 LEU12 LEU19 LEU26 e GLU6 LEU13 GLU20 LYS27 f ASP7 SER14 ASN21 LYS28 g LYS8 LYS15 GLU22 LEU29
Ion pairs
Lys15 Glu20' Glu22 Lys27' Glu22' Lys27
Crossing Angle ~18o
Molecular Surface of GCN4
3D Demonstrations
Tour of Heptad Repeat (3D Studio MAX)
Tour of GCN4 (Swiss-PDB)
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
3-Stranded Coiled Coil!?
(parallel)
Axial symmetry Hydrophobic core
Ion pairs b
f d c g a e b f d g c c g e a d a e f b
Figure adapted from Cohen, C., and D.A. D. Perry, "D-helical coiled coils and bundles: How to design an D-helical protein." PROTEINS: Structure, Function, and Genetics 7 (1990): 1-15.
4-Stranded Coiled Coil!?
(parallel)
f
Axial symmetry Hydrophobic core
Ion pairs b
f d c g e
Figure adapted from Cohen, C., and D.A.D. Perry, "D-helical coiled coils and bundles: How to design an D-helical protein." PROTEINS: Structure, Function, and Genetics 7 (1990): 1-15.
c g e a d a
b e g d f a a d g e b c
b f
c
Recall - GCN4
Hydrophobic core:
"a" (blue) Val9 Asn16 Val23 Val30 "d" (red) Leu5 Leu12 Leu19 Leu26
Harbury, P. B., Tao Zhang, Peter S. Kim, and Tom Alber. "A Switch Between Two-, Three-, and Four-Stranded Coiled Coils in GCN4 Leucine Zipper Mutants." Science 262 (1993): 1401-1407.
Mutagenized Hydrophobic Core
p-LI ( X => Leu - volume-preserving)
"a" "d" Leu9 Ile5 Leu16 Ile12 Leu23 Ile19 Leu30 Ile26 => tetramer (parallel) !!
Mutant p-LI
GCN4 P-LI
GCN4 p-LI
Ion pairs/salt bridges
`e' & `g' (5/12)
GluB6 ArgA1
g e a f d c g e b f c a d g a e b d a d f f c b e g c
`g' & `b' (4/8)
LysD8 GluA10
b
`e' & `c' (5/8)
HisB18 GluC20