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Cited by 43Protein Structure and Dynamicsnanoparticles nucleation surface interactionsAtmospheric aerosols and clouds

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Structure and Protein-Protein Interactions of Ice Nucleation Proteins Drive Their Activity

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Hartmann, Susan, Ling, Meilee, Dreyer, Lasse S. A., Zipori, Assaf, Finster, Kai, Grawe, Sarah, Jensen, Lasse Z., Borck, Stella, Reicher, Naama, Drace, Taner, Niedermeier, Dennis, Jones, Nykola C., Hoffmann, Søren V., Wex, Heike, Rudich, Yinon, Boesen, Thomas, Šantl-Temkiv, Tina·2022·Frontiers in Microbiology
DOI 10.3389/fmicb.2022.872306PMC PMC9247515

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Abstract

Microbially-produced ice nucleating proteins (INpro) are unique molecular structures with the highest known catalytic efficiency for ice formation. Airborne microorganisms utilize these proteins to enhance their survival by reducing their atmospheric residence times. INpro also have critical environmental effects including impacts on the atmospheric water cycle, through their role in cloud and precipitation formation, as well as frost damage on crops. INpro are ubiquitously present in the atmosphere where they are emitted from diverse terrestrial and marine environments. Even though bacterial genes encoding INpro have been discovered and sequenced decades ago, the details of how the INpro molecular structure and oligomerization foster their unique ice-nucleation activity remain elusive. Using machine-learning based software AlphaFold 2 and trRosetta, we obtained and analysed the first ab initio structural models of full length and truncated versions of bacterial INpro. The modeling revealed a novel beta-helix structure of the INpro central repeat domain responsible for ice nucleation activity. This domain consists of repeated stacks of two beta strands connected by two sharp turns. One beta-strand is decorated with a TxT amino acid sequence motif and the other strand has an SxL[T/I] motif. The core formed between the stacked beta helix-pairs is unusually polar and very distinct from previous INpro models. Using synchrotron radiation circular dichroism, we validated the β-strand content of the central repeat domain in the model. Combining the structural model with functional studies of purified recombinant INpro, electron microscopy and modeling, we further demonstrate that the formation of dimers and higher-order oligomers is key to INpro activity. Using computational docking of the new INpro model based on rigid-body algorithms we could reproduce a previously proposed homodimer structure of the INpro CRD with an interface along a highly conserved tyrosine ladder and show that the dimer model agrees with our functional data. The parallel dimer structure creates a surface where the TxT motif of one monomer aligns with the SxL[T/I] motif of the other monomer widening the surface that interacts with water molecules and therefore enhancing the ice nucleation activity. This work presents a major advance in understanding the molecular foundation for bacterial ice-nucleation activity.

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Metadata

Authors
Hartmann, S., Ling, M., Dreyer, L. S. A., Zipori, A., Finster, K., Grawe, S., Jensen, L. Z., Borck, S., Reicher, N., Drace, T., Niedermeier, D., Jones, N. C., Hoffmann, S. V., Wex, H., Rudich, Y., Boesen, T., & Šantl-Temkiv, T.
Affiliations
  • Leibniz Institute for Tropospheric Research (DE)
  • Aarhus University (DK)
  • Weizmann Institute of Science (IL)
Corresponding author
Boesen, Thomas
ORCID
Venue
Frontiers in Microbiology
Publisher
Frontiers Media SA
Published
2022-06-17
Volume
13
Pages
872306-872306
ISSN
1664-302X (ISSN-L)
DOI
10.3389/fmicb.2022.872306
PMC
PMC9247515
OpenAlex
W4283018332
Cited by
43
References
2
Citations by year
2026: 9 · 2025: 9 · 2024: 9 · 2023: 14 · 2022: 2
FWCI
2.78
Type
journal article
Language
en
Open access
Licence
Locations
  • Frontiers in Microbiology (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
  • Danish National Research Foundation (DNRF106)
  • Villum Fonden (23175, 37435)
  • Novo Nordisk (NNF19OC0056963)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Chemistry › Physical and Theoretical Chemistry › nanoparticles nucleation surface interactions
  • Physical Sciences › Environmental Science › Global and Planetary Change › Atmospheric aerosols and clouds
Keywords
ice nucleation protein, bacterial ice nucleators, protein structure, protein-protein interaction, oligomerization, homodimer, airborne microorganisms, cloud formation, frost damage

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