Research ArticleNANOMATERIALS

Computationally designed peptides for self-assembly of nanostructured lattices

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Science Advances  09 Sep 2016:
Vol. 2, no. 9, e1600307
DOI: 10.1126/sciadv.1600307
  • Fig. 1 Computationally designed, helical, homotetramer assemblies.

    (A to D) Models of peptides forming distinct nanostructures using a de novo designed helical homotetramer motif, which comprises both the backbone coordinates of the D2 symmetric tetramer and interior hydrophobic residues. On the left of each panel, designed exterior residues are colored according to chemical properties: positively charged KHR (blue), negatively charged DE (red), polar NQSTY (green), hydrophobic FILMVW (yellow), and small AG (cyan). Interior hydrophobic residues common to all the sequences are gray. On the right of each panel, the targeted assemblies are rendered along with symmetry axes (C2, oval; C3, triangle; C4, square; C6, hexagon) and the unique dimensions of the unit cell, a and b. (A) D2 symmetric tetramer designed in isolation and targeted to remain not assembled in solution. The exterior residues of the remaining proteins were designed in the context of a single layer from the corresponding space groups (B) P622, (C) P422, and (D) P222.

  • Fig. 2 Structural characterization of assemblies comprising designed peptides.

    (A) Small-angle neutron scattering data and nanocylinder fit (black curve) of BNDL_1 assembled from 5 mM peptide solution in borate buffer (pH 10). Fit provides a cylinder length of ~3.5 nm and a radius of ~1 nm, consistent with tetrameric coiled coil soluble bundle design. (B to D) Peptide solutions were heated to 80°C to obviate intermolecular or intramolecular structures and then allowed to cool to room temperature for intermolecular assembly. (B) Left: Low-magnification cast-film transmission electron microscopy (TEM) image of P622_6 assembled from 1 mM peptide solution in phosphate buffer (pH 7). (B) Right: High-magnification image of negatively stained lattice consistent with P622 symmetry. Upper inset is the fast Fourier transform (FFT) calculated from the high-magnification TEM data, whereas the lower inset is the inverse FFT (IFFT) calculated using the FFT maxima. (C) Left: Low-magnification cast-film TEM image of P422_1 assembled from 1 mM peptide solution in borate buffer (pH 10). (C) Right: High-magnification image of negatively stained lattice. Upper and lower insets are the FFT and IFFT, respectively. (D) Left: Low-magnification cast-film image of P222_1 assembled from 1 mM peptide solution in phosphate buffer (pH 7). (D) Right: High-magnification image of positively stained lattice. Upper and lower insets are the FFT and IFFT, respectively.

  • Fig. 3 Cast-film TEM examples of morphology control with manipulation of solution assembly conditions and peptide primary structure.

    All sample solutions heated to above 80°C for 1 hour to obviate any assembled or secondary structure before respective cooling treatment. (A and B) P622_2 peptide (0.5 mM) at pH 7 (phosphate buffer) quenched to (A) 50°C versus (B) 25°C and imaged after 1 day. (C and D) P222_9 (1.0 mM) ambiently cooled to room temperature at (C) pH 7 (phosphate buffer) versus (D) pH 10 (borate buffer) showing a clear difference in superstructure growth. (E and F) Plates grown from 0.1 mM peptide solutions with peptide primary structure altered through acetylation of the N terminus. Ambient cooling to room temperature allowing assembly of (E) P222_9_Ac at a low pH of 4.5 in sodium acetate buffer and of (F) P422_1_Ac quenched to 50°C at pH 8 in phosphate buffer. (G and H) Plates grown from 1.0 mM peptide solutions at pH 7 (phosphate buffer) after ambient cooling to room temperature, with P222_9 peptide primary structure altered through addition of (G) four glycines versus (H) six glycines to the N terminus of the P222_9 peptide molecule.

  • Table 2 Lattice parameters of the self-assembling peptides from the design in comparison with those determined from analysis of Fourier transforms of the TEM images in Fig. 2.

    a and b denote the dimensions of the two-dimensional unit cell, and γ denotes the interior angle defined by sides a and b.

    DesignTEM
    a (nm)b (nm)γ (°)a (nm)b (nm)γ (°)
    P622_64.574.571204.5 ± 0.34.5 ± 0.3112.7 ± 0.4
    P422_13.123.12904.2 ± 0.23.9 ± 0.288.9 ± 0.9
    P222_12.092.00903.3 ± 0.33.2 ± 0.3100.4 ± 0.9

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/2/9/e1600307/DC1

    Supplementary Materials and Methods

    fig. S1. Representative backbone configurations of the helix bundle motif building block illustrating the variation of the geometric parameters associated with the bundle.

    fig. S2. Side view and top view of the selected low-energy helix bundle motif with the most probable amino acids at the interior sites shown in space-filling representations.

    fig. S3. P422_1 analytical HPLC.

    fig. S4. P422_1_ac analytical HPLC.

    fig. S5. P222_9 analytical HPLC.

    fig. S6. P222_9 sequence (3168 daltons).

    fig. S7. P422_1 sequence (3572 daltons).

    fig. S8. BNDL_1 (3560 daltons).

    fig. S9. P622_6 (3517 daltons).

    fig. S10. P222_9 (0.1 mM) in borate buffer (pH 10) on heating.

    fig. S11. P622_6 (0.1 mM) in phosphate buffer (pH 7) on heating.

    fig. S12. BNDL_1 (0.1 mM) in borate buffer (pH 10) on heating.

    fig. S13. P422_1 (0.1 mM) in borate buffer (pH 10).

    fig. S14. AUC data and analysis of BNDL_1.

    fig. S15. High-magnification TEM of 1.0 mM P222_9 ambiently cooled to room temperature from 80°C at pH 7 (left) and pH 10 (right).

    fig. S16. High-magnification TEM of (left) lattice of P222_9_Ac at pH 7 ambiently cooled to room temperature from 80°C and (right) P422_1_Ac at pH 8 quenched to 40°C from 80°C.

    fig. S17. High-magnification TEM of lattice of P222_9_6Gly at pH 7 ambiently cooled to room temperature from 80°C.

    fig. S18. Putative structure of assembly of P422_1 helix bundles packed with P4 symmetry, which is a local minimum within the structure energy landscape with respect to variation of the unit cell parameter.

    fig. S19. Putative assembly structures of P222_1 assemblies with P2 symmetry located at a local minimum of the structure energy landscape with respect to variation of the unit cell parameters.

    References (3952)

  • Supplementary Materials

    This PDF file includes:

    • Supplementary Materials and Methods
    • fig. S1. Representative backbone configurations of the helix bundle motif building block illustrating the variation of the geometric parameters associated with the bundle.
    • fig. S2. Side view and top view of the selected low-energy helix bundle motif with the most probable amino acids at the interior sites shown in space-filling representations.
    • fig. S3. P422_1 analytical HPLC.
    • fig. S4. P422_1_ac analytical HPLC.
    • fig. S5. P222_9 analytical HPLC.
    • fig. S6. P222_9 sequence (3168 daltons).
    • fig. S7. P422_1 sequence (3572 daltons).
    • fig. S8. BNDL_1 (3560 daltons).
    • fig. S9. P622_6 (3517 daltons).
    • fig. S10. P222_9 (0.1 mM) in borate buffer (pH 10) on heating.
    • fig. S11. P622_6 (0.1 mM) in phosphate buffer (pH 7) on heating.
    • fig. S12. BNDL_1 (0.1 mM) in borate buffer (pH 10) on heating.
    • fig. S13. P422_1 (0.1 mM) in borate buffer (pH 10).
    • fig. S14. AUC data and analysis of BNDL_1.
    • fig. S15. High-magnification TEM of 1.0 mM P222_9 ambiently cooled to room temperature from 80°C at pH 7 (left) and pH 10 (right).
    • fig. S16. High-magnification TEM of (left) lattice of P222_9_Ac at pH 7 ambiently cooled to room temperature from 80°C and (right) P422_1_Ac at pH 8 quenched to 40°C from 80°C.
    • fig. S17. High-magnification TEM of lattice of P222_9_6Gly at pH 7 ambiently cooled to room temperature from 80°C.
    • fig. S18. Putative structure of assembly of P422_1 helix bundles packed with P4 symmetry, which is a local minimum within the structure energy landscape with respect to variation of the unit cell parameter.
    • fig. S19. Putative assembly structures of P222_1 assemblies with P2 symmetry located at a local minimum of the structure energy landscape with respect to variation of the unit cell parameters.
    • References (3952)

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