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Near-atomic-resolution structure of J-aggregated helical light-harvesting nanotubes

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Abstract

Cryo-electron microscopy has delivered a resolution revolution for biological self-assemblies, yet only a handful of structures have been solved for synthetic supramolecular materials. Particularly for chromophore supramolecular aggregates, high-resolution structures are necessary for understanding and modulating the long-range excitonic coupling. Here, we present a 3.3 Å structure of prototypical biomimetic light-harvesting nanotubes derived from an amphiphilic cyanine dye (C8S3-Cl). Helical 3D reconstruction directly visualizes the chromophore packing that controls the excitonic properties. Our structure clearly shows a brick layer arrangement, revising the previously hypothesized herringbone arrangement. Furthermore, we identify a new non-biological supramolecular motif—interlocking sulfonates—that may be responsible for the slip-stacked packing and J-aggregate nature of the light-harvesting nanotubes. This work shows how independently obtained native-state structures complement photophysical measurements and will enable accurate understanding of (excitonic) structure–function properties, informing materials design for light-harvesting chromophore aggregates.

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Fig. 1: LHNs of amphiphilic cyanine dye C8S3-Cl.
Fig. 2: Cryo-EM density maps of the LHNs.
Fig. 3: Molecular model for the inner wall LHNs.
Fig. 4: Dimerized Frenkel exciton model for the inner wall.
Fig. 5: Impact of chemical modifications on the self-assembly.

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Data availability

All data required to interpret, verify and extend the results are given in the paper and its Supplementary Information. The map of both outer and inner wall LHNs is deposited in the Electron Microscopy Data Bank under accession code EMD-27820. The PDB file for inner wall structure is given in Supplementary Data 1. Source data are provided with this paper.

Code availability

Codes for the model used in the paper are available from the corresponding author upon reasonable request.

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Acknowledgements

This work was funded by National Science Foundation Division of Chemistry grant 2204263 (E.M.S. and J.R.C.) and National Institutes of Health grant GM122510 (E.H.E.). A.P.D. thanks the University of California, Los Angeles Graduate Division Dissertation Year Fellowship for financial support. The authors acknowledge the use of the University of California, Los Angeles-Department of Energy Biochemistry Instrumentation Core Facility and University of California, Los Angeles Molecular Instrumentation Center. C.C. acknowledges start-up funding from University of Nevada, Las Vegas.

Author information

Author notes

  1. These authors contributed equally: Arundhati P. Deshmukh, Weili Zheng.

  2. These authors jointly supervised this work: Edward H. Egelman, Justin R. Caram.

Authors and Affiliations

  1. Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA

    Arundhati P. Deshmukh, Austin D. Bailey, Jillian A. Williams, Ellen M. Sletten & Justin R. Caram

  2. Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA

    Weili Zheng & Edward H. Egelman

  3. Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario, Canada

    Chern Chuang

  4. Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA

    Chern Chuang

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  1. Arundhati P. Deshmukh
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Contributions

A.P.D. was responsible for preparing the first draft, editing, conceptualization, LHNs spectroscopy and sample preparation. W.Z. was responsible for cryo-EM imaging and reconstruction and editing. C.C. was responsible for dimerized Frenkel exciton model, outer wall model, writing and editing. A.D.B. was responsible for synthesis of chemically modified dyes, isolated inner wall sample prep and spectroscopy and editing. J.A.W. was responsible for aggregate screening and cryo-EM imaging of C8S4-Cl and C8S3-Br and editing. E.M.S. was responsible for advising and editing. E.H.E. was responsible for advising, editing and conceptualization. J.R.C. was responsible for advising, editing and conceptualization.

Corresponding author

Correspondence to Justin R. Caram.

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Extended data

Extended Data Table 1 A literature survey of structural investigations on the LHNs
Full size table

Extended Data Fig. 1 Structure of inner wall asymmetric unit.

Left: Inner wall asymmetric unit (hydrogen atoms are omitted for clarity) obtained from the refined inner wall model, right: the corresponding ChemDraw structure.

Extended Data Fig. 2 Circular dichroism spectra of identical LHN samples.

Circular dichroism spectra of four identical LHN samples in 30% MeOH:H2O mixtures and 0.43 mM final dye concentration.

Source data

Extended Data Fig. 3 Zoomed-in inner wall density.

Cut away top-down view of the inner wall. The sulfonate lobes (denoted by black arrows) show a regular interlocked pattern.

Extended Data Fig. 4 Outer wall molecular model.

Outer wall density overlayed with the fitted molecular model with manual constraints. a. side view, b. cut-away view, and c. asymmetric unit (ASU). The sulfonate interlocking can be seen in the outer wall as well.

Extended Data Fig. 5 Calculated spectra from the dimerized Frenkel exciton model.

a. Absorption, b. linear dichroism, and c. circular dichroism spectra of isolated inner walls of the LHNs. Solid black lines: experimental spectra; colored lines: spectra calculated from the dimerized Frenkel exciton Hamiltonian corresponding to inner wall structures of varying sizes, blue: 1500, red: 3000, yellow: 4500, and purple: 6000 monomers; dashed black lines: calculated spectra assuming periodic boundary conditions with added Lorentizian broadenings. The lineshape of the perpendicular peaks depends more strongly on the tube length truncation than their parallel counterparts which could possibly introduce more lineshape mismatch for the perpendicular peaks.

Source data

Extended Data Fig. 6 C8S3-Br nanotubes self-assembly over long time.

a Dynamic light scattering (DLS) intensity distributions of C8S3-Br nanotubes in solutions (20% MeOH v/v in MeOH:H2O mixture with 0.2 mM dye concentration) at various time intervals after aggregate preparation. The distribution depicts shorter lengths initially at 10 min and then shifts to drastically longer lengths over a course of 5 weeks. We note that the DLS scattering intensities are related to the hydrodynamic diameters of the freely diffusing nanotubes and can be used to estimate the length of the nanotubes, b. normalized absorption spectra corresponding to each time point showing a slow conversion from nanotubes to bundles, c. and d. representative cryo-EM images of the samples frozen 1 day and 5 weeks after aggregate preparation, respectively.

Source data

Extended Data Fig. 7 C8S4-Cl aggregate absorption spectra over a week.

a. Absorption spectra of C8S4-Cl aggregates made at 0.1 mM dye concentration and 5% MeOH over a course of 7 days showing conversion to sheet-like morphology, and b. normalized absorption spectra of the monomer in 100% MeOH (black), sheets in 20% MeOH (blue) and tubes in 5% MeOH (red) with 0.1 mM final dye concentration.

Source data

Supplementary information

Supplementary Information

Dimerized Frenkel exciton model, geometric model for C8S3-Br, synthesis details for C8S4-Cl and table of cryo-EM data collection.

Supplementary Data 1

Co-ordinates file for the inner wall structure.

Source data

Source Data Fig. 1

Absorption spectra of C8S3-Cl monomer and LHNs; linear dichroism spectra of the isolated inner walls.

Source Data Fig. 4

Calculated and experimental spectra for the isolated inner wall.

Source Data Fig. 5

C8S3-Cl and C8S3-Br aggregate absorptions, tube widths, FFT C8S3-Br tube widths, C8S3-Cl and C8S4-Cl aggregate absorptions.

Source Data Extended Data Fig. 2

Circular dichroism spectra of the LHNs.

Source Data Extended Data Fig. 5

Calculated and experimental spectra for the isolated inner wall with different sizes of the tubes.

Source Data Extended Data Fig. 6

DLS and aggregate absorption spectra over time for C8S3-Br.

Source Data Extended Data Fig. 7

Absorption spectra of C8S4-Cl over time, normalized spectra of C8S4-Cl sheets, tubes and monomers.

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Deshmukh, A.P., Zheng, W., Chuang, C. et al. Near-atomic-resolution structure of J-aggregated helical light-harvesting nanotubes. Nat. Chem. (2024). https://doi.org/10.1038/s41557-023-01432-6

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