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Coiled Coils

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

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Coiled Coils

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  1. Coiled Coils 7.88J Protein Folding Prof. David Gossard Room 3-336, x3-4465 Gossard@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 7:1-15.

  4. 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

  5. Coiled Coils • Left-handed spiral of right-handed helices • May be parallel or anti-parallel N C N C C N N C

  6. Equations of Helix (Coil) = tan –1 (2pr0/p0) ro - radius Po - pitch a = pitch angle

  7. 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

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

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

  10. Features of Coiled Coil • Heptad repeat in sequence • [a b c de 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” +/-

  11. 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 7:1-15 (1990)

  12. Heptad Repeat in 3D Charged residues +/- g -/+ +/- e g c f f d d b e a b c a -/+ Hydrophobic residues

  13. Hydrophobic Core is on Axis of Superhelix ( ~Straight) d d a a

  14. Charged Residues Provide Stability, Registration Charged residues “e” and “g” Ion pairs between coils

  15. Demonstration • Heptad repeat in 3D • Full Coiled Coil in 3D • “Knobs in Holes” Packing

  16. 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

  17. GCN4-p1 Leucine Zipper (2ZTA) • Residues contain heptad repeat • Ion pairs • Lys15 – Glu20’ • Glu22 – Lys27’ • Glu22’ – Lys27

  18. Crossing Angle ~18o

  19. 3-Stranded Coiled Coil!? (parallel) • Axial symmetry • Hydrophobic core • Ion pairs

  20. 4-Stranded Coiled Coil!? (parallel) • Axial symmetry • Hydrophobic core • Ion pairs

  21. 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

  22. END

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