Research ArticleBIOCHEMISTRY

Gold nanocrystal labels provide a sequence–to–3D structure map in SAXS reconstructions

See allHide authors and affiliations

Science Advances  25 May 2018:
Vol. 4, no. 5, eaar4418
DOI: 10.1126/sciadv.aar4418
  • Fig. 1 Schematic of SAXS measurements and workflow to determine gold label positions in macromolecular reconstructions.

    (A) Schematic of SAXS measurements. The incident synchrotron-generated x-ray beam (red line) is shown with x-ray optics. Single gold-labeled macromolecules are placed into the x-ray beam in a sample cell. The direct beam is blocked by a beam stop, and scattered photons are detected using a charge-coupled device (CCD) detector. (B) Scattering intensity equation for a single labeled molecule. The scattering signal can be decomposed into a sum of the individual scattering contributions: the gold label scattering, the gold-macromolecule cross-term, and the scattering from the macromolecule only. (C) Schematic of the workflow to determine the positions of gold labels relative to low-resolution three-dimensional (3D) reconstructions of unlabeled macromolecules. The SAXS profile of the unlabeled sample is used in ab initio reconstruction of a low-resolution model consisting of dummy residues or beads. Sterically allowed gold label trial positions are computed in the bead model. Experimental data from the gold-labeled sample are compared to the computed scattering profile for each of the trial positions, and the best-fitting positions are identified.

  • Fig. 2 SAXS shape reconstruction, trial gold label positions, and computed scattering intensity profiles.

    (A and B) SAXS profiles and Guinier fits for representative samples [20-bp end-labeled DNA in (A) and calmodulin labeled at position N111C in (B)]. Experimental SAXS profiles are shown as circles and the number of s-bins is reduced for clarity. Guinier fits to determine I(0) are shown as solid lines. (C and D) 3D reconstructions of 20-bp DNA in (C) and calmodulin in (D). The known high-resolution structures are superimposed (27). (E and F) Trial gold label positions (blue spheres) calculated around the envelope of the 3D reconstruction for the 20-bp DNA (E) and calmodulin (F). (G and H) Calculated total intensity profiles for a reduced set of trial gold label positions for 20-bp DNA (G) and calmodulin (H). All trial profiles were ordered from the best to the worst fitting, and every 20th curve is shown for clarity, resulting in 91 traces for 20-bp DNA (G) and 1200 traces for calmodulin (H).

  • Fig. 3 Determination of gold label positions for end-labeled DNA.

    (A) Secondary structure of the 35-bp DNA duplex and the gold label position indicated on the 3′ end of the upper strand. (B) Mapping gold label positions to 3D reconstructions using SAXS data for end-labeled DNA. Left column: Schematic representations of the 10-, 15-, 20-, 25-, 30-, and 35-bp DNA constructs end-labeled with gold nanocrystals used in the study. Middle and right columns: Side (middle) and front (right) views of the 3D reconstructions of the unlabeled samples (shown as gray spheres) and mapped positions of the gold labels (blue to red spheres; blue spheres correspond to the best fit). The placement of the gold labels at the end and off-center is reproduced well.

  • Fig. 4 Determination of gold label positions for internally labeled DNA.

    (A) Secondary structure of the 26-bp DNA duplex. Colored letters indicate bases used for internal labeling. The same color code is used in (B) and (C). (B) Low-resolution shape reconstructions of the unlabeled DNA (gray) superimposed on a high-resolution structure. The best-fitting label positions for the six different internal gold label positions are shown as colored spheres. (C) Distance to the center of the DNA computed as the mean and SD of the best 50 reconstructed and filtered label positions for each attachment point as a function of the distance of the labeled base from the center of the helix [converted using a helical rise per base of 3.3 Å (16, 17)]. The dashed line indicates 45°. The RMSD between computed and expected positions is 2.1 Å.

  • Fig. 5 Gold label positions for an RNA kink-turn motif.

    (A) Secondary structure of the RNA kink-turn and the two labeling positions at the 3′ ends for the individual constructs. The 3-nt kink-turn bulge is displayed with a small vertical offset, and the three-base mismatch region is shown in orange. (B) Shape reconstruction of the unlabeled RNA kink-turn (light gray shape) superimposed with the high-resolution structure (22). (C) Low-resolution model (gray spheres) and best-fitting gold nanocrystal positions (blue and red spheres) after filtering. (D) Scatter plot of filtered gold label positions. The x axis value of the fitted label positions is plotted versus the overall distance to the geometrical center of the low-resolution shape reconstruction.

  • Fig. 6 Gold label position reconstructions for labeled calmodulin constructs.

    (A) Crystal structure of Ca2+-bound calmodulin (27) with mutated amino acid positions indicated by colored spheres (R37, blue; N111, red). (B) View of the 3D reconstructions of the unlabeled protein (shown as brown spheres) and mapped positions of the gold labels at R37C (blue) and N111C (red) as colored spheres for the filtered final label positions. The placement of the gold labels at the designated positions is well reproduced.

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/4/5/eaar4418/DC1

    fig. S1. Radius distribution of gold nanocrystals.

    fig. S2. SAXS scattering profiles of end-labeled DNA samples for label position reconstruction.

    fig. S3. SAXS scattering profiles of the full set of DNA samples for internal label position reconstruction.

    fig. S4. SAXS scattering profiles of two end-labeled RNA kink-turn motif samples.

    fig. S5. SAXS data for unlabeled calmodulin.

    fig. S6. Pair-distance distributions for all unlabeled and labeled samples.

    fig. S7. SAXS scattering profiles of two different labeled calmodulin samples.

    fig. S8. Spread of the best-fitting position depending on the initial trial point density.

    table S1. DNA sequences used in the experiments on end-labeled DNA.

    table S2. DNA sequences used in the experiments with internally labeled DNA.

    table S3. RNA kink-turn sequence.

    table S4. Radii of gyration Rg values for all unlabeled and labeled samples.

  • Supplementary Materials

    This PDF file includes:

    • fig. S1. Radius distribution of gold nanocrystals.
    • fig. S2. SAXS scattering profiles of end-labeled DNA samples for label position reconstruction.
    • fig. S3. SAXS scattering profiles of the full set of DNA samples for internal label position reconstruction.
    • fig. S4. SAXS scattering profiles of two end-labeled RNA kink-turn motif samples.
    • fig. S5. SAXS data for unlabeled calmodulin.
    • fig. S6. Pair-distance distributions for all unlabeled and labeled samples.
    • fig. S7. SAXS scattering profiles of two different labeled calmodulin samples.
    • fig. S8. Spread of the best-fitting position depending on the initial trial point density.
    • table S1. DNA sequences used in the experiments on end-labeled DNA.
    • table S2. DNA sequences used in the experiments with internally labeled DNA.
    • table S3. RNA kink-turn sequence.
    • table S4. Radii of gyration Rg values for all unlabeled and labeled samples.

    Download PDF

    Files in this Data Supplement:

Navigate This Article