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Directing polymorph specific calcium carbonate formation with de novo protein templates

Author

Listed:
  • Fatima A. Davila-Hernandez

    (University of Washington
    University of Washington
    University of Washington)

  • Biao Jin

    (Pacific Northwest National Laboratory
    University of Washington)

  • Harley Pyles

    (University of Washington
    University of Washington)

  • Shuai Zhang

    (Pacific Northwest National Laboratory
    University of Washington)

  • Zheming Wang

    (Pacific Northwest National Laboratory)

  • Timothy F. Huddy

    (University of Washington
    University of Washington)

  • Asim K. Bera

    (University of Washington
    University of Washington)

  • Alex Kang

    (University of Washington
    University of Washington)

  • Chun-Long Chen

    (Pacific Northwest National Laboratory
    University of Washington)

  • James J. Yoreo

    (Pacific Northwest National Laboratory
    University of Washington)

  • David Baker

    (University of Washington
    University of Washington
    University of Washington)

Abstract

Biomolecules modulate inorganic crystallization to generate hierarchically structured biominerals, but the atomic structure of the organic-inorganic interfaces that regulate mineralization remain largely unknown. We hypothesized that heterogeneous nucleation of calcium carbonate could be achieved by a structured flat molecular template that pre-organizes calcium ions on its surface. To test this hypothesis, we design helical repeat proteins (DHRs) displaying regularly spaced carboxylate arrays on their surfaces and find that both protein monomers and protein-Ca2+ supramolecular assemblies directly nucleate nano-calcite with non-natural {110} or {202} faces while vaterite, which forms first in the absence of the proteins, is bypassed. These protein-stabilized nanocrystals then assemble by oriented attachment into calcite mesocrystals. We find further that nanocrystal size and polymorph can be tuned by varying the length and surface chemistry of the designed protein templates. Thus, bio-mineralization can be programmed using de novo protein design, providing a route to next-generation hybrid materials.

Suggested Citation

  • Fatima A. Davila-Hernandez & Biao Jin & Harley Pyles & Shuai Zhang & Zheming Wang & Timothy F. Huddy & Asim K. Bera & Alex Kang & Chun-Long Chen & James J. Yoreo & David Baker, 2023. "Directing polymorph specific calcium carbonate formation with de novo protein templates," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-43608-1
    DOI: 10.1038/s41467-023-43608-1
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    References listed on IDEAS

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    1. TJ Brunette & Fabio Parmeggiani & Po-Ssu Huang & Gira Bhabha & Damian C. Ekiert & Susan E. Tsutakawa & Greg L. Hura & John A. Tainer & David Baker, 2015. "Exploring the repeat protein universe through computational protein design," Nature, Nature, vol. 528(7583), pages 580-584, December.
    2. Yang Hsia & Rubul Mout & William Sheffler & Natasha I. Edman & Ivan Vulovic & Young-Jun Park & Rachel L. Redler & Matthew J. Bick & Asim K. Bera & Alexis Courbet & Alex Kang & T. J. Brunette & Una Nat, 2021. "Design of multi-scale protein complexes by hierarchical building block fusion," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    3. Brian Koepnick & Jeff Flatten & Tamir Husain & Alex Ford & Daniel-Adriano Silva & Matthew J. Bick & Aaron Bauer & Gaohua Liu & Yojiro Ishida & Alexander Boykov & Roger D. Estep & Susan Kleinfelter & T, 2019. "De novo protein design by citizen scientists," Nature, Nature, vol. 570(7761), pages 390-394, June.
    4. Po-Ssu Huang & Scott E. Boyken & David Baker, 2016. "The coming of age of de novo protein design," Nature, Nature, vol. 537(7620), pages 320-327, September.
    5. Guomin Zhu & Maria L. Sushko & John S. Loring & Benjamin A. Legg & Miao Song & Jennifer A. Soltis & Xiaopeng Huang & Kevin M. Rosso & James J. De Yoreo, 2021. "Self-similar mesocrystals form via interface-driven nucleation and assembly," Nature, Nature, vol. 590(7846), pages 416-422, February.
    6. Wenge Jiang & Michael S. Pacella & Dimitra Athanasiadou & Valentin Nelea & Hojatollah Vali & Robert M. Hazen & Jeffrey J. Gray & Marc D. McKee, 2017. "Chiral acidic amino acids induce chiral hierarchical structure in calcium carbonate," Nature Communications, Nature, vol. 8(1), pages 1-13, April.
    7. Harley Pyles & Shuai Zhang & James J. De Yoreo & David Baker, 2019. "Controlling protein assembly on inorganic crystals through designed protein interfaces," Nature, Nature, vol. 571(7764), pages 251-256, July.
    8. Lyle M. Gordon & Derk Joester, 2011. "Nanoscale chemical tomography of buried organic–inorganic interfaces in the chiton tooth," Nature, Nature, vol. 469(7329), pages 194-197, January.
    9. V. Saderne & N. R. Geraldi & P. I. Macreadie & D. T. Maher & J. J. Middelburg & O. Serrano & H. Almahasheer & A. Arias-Ortiz & M. Cusack & B. D. Eyre & J. W. Fourqurean & H. Kennedy & D. Krause-Jensen, 2019. "Role of carbonate burial in Blue Carbon budgets," Nature Communications, Nature, vol. 10(1), pages 1-9, December.
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