De novo designed ice-binding proteins from twist-constrained helices

Robbert J. de Haas, Roderick P. Tas, Daniëlle van den Broek, Chuanbao Zheng, Hannah Nguyen, Alex Kang, Asim K. Bera, Neil P. King, Ilja K. Voets (Corresponding author), Renko de Vries (Corresponding author)

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Abstract

Attaining molecular-level control over solidification processes is a crucial aspect of materials science. To control ice formation, organisms have evolved bewildering arrays of ice-binding proteins (IBPs), but these have poorly understood structure-activity relationships. We propose that reverse engineering using de novo computational protein design can shed light on structure-activity relationships of IBPs. We hypothesized that the model alpha-helical winter flounder antifreeze protein uses an unusual undertwisting of its alpha-helix to align its putative ice-binding threonine residues in exactly the same direction. We test this hypothesis by designing a series of straight three-helix bundles with an ice-binding helix projecting threonines and two supporting helices constraining the twist of the ice-binding helix. Our findings show that ice-recrystallization inhibition by the designed proteins increases with the degree of designed undertwisting, thus validating our hypothesis, and opening up avenues for the computational design of IBPs.

Original languageEnglish
Article numbere2220380120
Number of pages8
JournalProceedings of the National Academy of Sciences of the United States of America
Volume120
Issue number27
DOIs
Publication statusPublished - 4 Jul 2023

Funding

Sciences from the NIH (P30 GM124165). This research used resources of the APS, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. ACKNOWLEDGMENTS. This work is supported financially by the VLAG graduate school research fellowship to R.J.d.H., the Dutch Research Council to R.P.T. (NWO-VENI 202.220), the European Research Council to I.K.V. (ERC-2020-CoG 101001965) and the Audacious Project at the Institute for Protein Design to N.P.K. We thank an anonymous reviewer for pointing out why the 11-mer is uniquely suited as an ice-binding motif. Crystallographic work was conducted at the Advanced Photon Source (APS) Northeastern Collaborative Access Team beamlines, which are funded by the National Institute of General Medical

FundersFunder number
National Institute of General Medical Sciences
U.S. Department of Energy
Office of Science
Argonne National LaboratoryDE-AC02-06CH11357
Academy of Pharmaceutical Sciences
European Research CouncilERC-2020-CoG 101001965
Nederlandse Organisatie voor Wetenschappelijk OnderzoekNWO-VENI 202.220

    Keywords

    • ice-binding proteins
    • ice-recrystallization inhibition
    • protein design
    • Antifreeze Proteins/chemistry
    • Animals
    • Ice
    • Caspase 1
    • Flounder

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