Molecular design of stapled pentapeptides as building blocks of self-assembled coiled coil–like fibers

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Science Advances  22 Jan 2021:
Vol. 7, no. 4, eabd0492
DOI: 10.1126/sciadv.abd0492
  • Fig. 1 Design of a stapled peptide as a building block of helical assemblies.

    (A) Chemical structures of the stapled peptide motif investigated in this study with its four modifiable groups highlighted in colors. (B) Helical wheel view of the stapled peptide. Seven faces of an ideal helix, which are respectively occupied by heptad sequence, are denoted as a to g. The bridges surrounding the wheel denote possible positions of the staple depending on how the pentapeptide sequence is mapped onto this ideal helical wheel. Those dashed bridges indicate the placement of the staple on the hydrophilic faces of the helix, which are thus discarded. The three potentially workable ways of mapping pentapeptide onto the helix and their corresponding helical wheel representations are shown in (C) and (D), respectively, with possible chemical modifications to the peptides summarized in (A).

  • Fig. 2 Molecular architecture of fiber segment of the designed stapled pentapeptide observed in simulations.

    (A) Representative structure of fiber segment. Shown as ellipsoids are peptide backbones. Peptides in the same helical columns are shown in the same color, and different helical columns are shown in different colors. (B) Details of local packing between peptides. O, N, C, and H atoms are shown in red, blue, gray, and white, respectively. Shown as orange and purple sticks are the staples and the App side chains at R4, respectively. Dashed double-headed arrows indicate the interchain side chain packing. Inset is a close-up view of head-to-tail interactions between peptides with the H1─O2 and H2─O1 HBs shown as dashed lines. (C) Map of atomic contact between peptides. In the axes of the plot, “r” denotes residue number, and “B” and “S” denote backbone and side chain, respectively. “Ph@R1” denotes the Ph at R1. “ACE” denotes the acetylated N-terminus. Two atoms of different peptides were thought to form contact if their distance is shorter than 4.5 Å. Dashed boxes highlighted the interpeptide contacts illustrated in (B). (D) Comparison of a long helix of heptad repeats (left) and a helical column of the pentapeptides (right). The head-to-tail HBs seen in (B) and their counterparts in the long helix are shown as dashed red lines. (E) Map of head-to-tail HBs. An HB is thought to occur if the donor-acceptor distance is <3.5 Å and the donor-hydrogen-acceptor angle is >120°. The chance of a particular HB type is calculated as nHB/(npepncol), where nHB is the number of HBs of this type and npep and ncol are the numbers of peptides and helical columns, respectively, seen in the aggregates. The results were averaged over the last microseconds of simulations. Shown on the right is the scale bar of probability.

  • Fig. 3 Growth of fiber segment into ribbon-like fiber observed in seeded simulations.

    (A and B) Shape of fiber assembly as a function of fiber size. Shown in (A) are the number of helical columns (red dots) and that of peptides in the longest column (black dots). Shown in (B) is the aspect ratio of the assembly. The results of two independent simulations are shown as solid and dashed lines, respectively. (C) Representative structures of fiber assemblies in different sizes and their cross sections. Shown as ellipsoids are peptide backbones with those in the same helical columns being in the same color and those in different helical columns being in different colors. The staples and the App side chains are shown as white and yellow ellipsoids, respectively. The numbers shown above each structure denote the count of peptides and helical columns, respectively. (D) Helical wheel representation of ribbon-like fiber observed in the simulations. The numbers in boldface indicate the order in which the columns emerged at the lateral edge of the fiber during the growth simulations. (E) Structures of single-ribbon (left) and triple-ribbon (right) models of fibers obtained at t = 100 ns of simulations. Gray arrows indicate the directions of fiber axes.

  • Fig. 4 Experimental characterization of molecular structures of fibrous assemblies of the designed stapled peptide.

    (A) CD spectrum of freshly prepared solution (2 mg/ml) of peptide 10. (B) Fourier transform infrared spectroscopy (FTIR) spectrum of assemblies of peptide 10 prepared at 2 mg/ml with sonification. SEM images of assemblies of peptide 10 prepared at 2 mg/ml with sonification (C) and through annealing (D). Red arrows in (C) highlighted fibers with a left-handed twist. (E) SEM images of annealed fibers prepared at 0.5 mg/ml. Insets show the branching ends of the fibers. (F) High-resolution TEM images of annealed fibers prepared at 0.5 mg/ml. (G) Close-up view of the fiber shown in the right panel of (F). The regions highlighted by dashed white boxes are amplified on the right. Short red lines illustrate the spacing between discrete strands aligned in the direction of fiber axis. (H) Projection of the triple-ribbon structure obtained from simulations onto the plane of sheet of helix. Each white dot represents a heavy atom. (I) Optical microscopy of the fibrous assemblies. From left to right, light microscopy and fluorescence microscopy using standard excitation wavelengths at 405, 440, 488, 514, and 561 nm.

  • Fig. 5 Fibrous assemblies formed by designed derivatives of peptide 10.

    SEM images of annealed fibrous assemblies formed by (A) A2K, (B) A3K, (C) A2E, and (D) A3E mutants of peptide 10. In each case, the right panel is a close-up view of the highlighted region in the left panel.

  • Table 1 Summary of the helicity and morphologies.

    The simulated and experimental helicity of pentapeptides examined in the present study and the morphologies of assemblies by these peptides according to simulations.

    1-MeAlaLeu0.71 ± 0.02*0.770.780.490.29
    2-PhAlaLeu0.54 ± 0.090.590.590.390.35
    3-MeLeuAla0.39 ± 0.080.42–†
    4-PhLeuAla0.41 ± 0.090.450.480.39
    5-MeAlaPhe0.27 ± 0.090.29
    6-PhAlaPhe0.19 ±
    7-MeAlaHpa0.68 ± 0.100.740.440.36
    8-PhAlaHpa0.58 ± 0.080.630.650.530.32
    9-MeAlaApp0.93 ±
    10-PhAlaApp0.92 ±
    11-MePheAla0.22 ± 0.070.24
    12-PhPheAla0.26 ±
    13-MeHpaAla0.34 ± 0.100.37
    14-PhHpaAla0.30 ± 0.100.33
    15-MeAppAla0.34 ± 0.090.370.590.39
    16-PhAppAla0.42 ± 0.050.46
    17-MeLeuLeu0.70 ± 0.060.760.370.32
    18-PhLeuLeu0.66 ± 0.020.720.340.42
    19-MeAppApp0.94 ±
    20-PhAppApp0.82 ± 0.100.890.250.36
    Derivatives of peptide 10
    21Ala2Lys (A2K)0.86 ± 0.080.930.960.940.06
    22Ala3Lys (A3K)0.95 ±
    23Ala2Glu (A2E)0.94 ±
    24Ala3Glu (A3E)0.95 ±

    *Uncertainty was determined as absolute difference in predicted helicities between REMD runs starting with full helical and nonhelical structures.

    †Not determined.

    ‡The results for peptides that can assemble into fiber segments are highlighted in boldface.

    Supplementary Materials

    • Supplementary Materials

      Molecular design of stapled pentapeptides as building blocks of self-assembled coiled coil–like fibers

      Yixiang Jiang, Wan Zhang, Fadeng Yang, Chuan Wan, Xiang Cai, Jianbo Liu, Qianling Zhang, Zigang Li, Wei Han

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      • Figs. S1 to S8
      • Tables S1 and S2

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