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Raffaelli T, Wilson DT, Dutertre S, Giribaldi J, Vetter I, Robinson SD, Thapa A, Widi A, Loukas A, Daly NL. Structural analysis of a U-superfamily conotoxin containing a mini-granulin fold: Insights into key features that distinguish between the ICK and granulin folds. J Biol Chem 2024; 300:107203. [PMID: 38508311 PMCID: PMC11035057 DOI: 10.1016/j.jbc.2024.107203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/28/2024] [Accepted: 03/14/2024] [Indexed: 03/22/2024] Open
Abstract
We are entering an exciting time in structural biology where artificial intelligence can be used to predict protein structures with greater accuracy than ever before. Extending this level of accuracy to the predictions of disulfide-rich peptide structures is likely to be more challenging, at least in the short term, given the tight packing of cysteine residues and the numerous ways that the disulfide bonds can potentially be linked. It has been previously shown in many cases that several disulfide bond connectivities can be accommodated by a single set of NMR-derived structural data without significant violations. Disulfide-rich peptides are prevalent throughout nature, and arguably the most well-known are those present in venoms from organisms such as cone snails. Here, we have determined the first three-dimensional structure and disulfide connectivity of a U-superfamily cone snail venom peptide, TxVIIB. TxVIIB has a VI/VII cysteine framework that is generally associated with an inhibitor cystine knot (ICK) fold; however, AlphaFold predicted that the peptide adopts a mini-granulin fold with a granulin disulfide connectivity. Our experimental studies using NMR spectroscopy and orthogonal protection of cysteine residues indicate that TxVIIB indeed adopts a mini-granulin fold but with the ICK disulfide connectivity. Our findings provide structural insight into the underlying features that govern formation of the mini-granulin fold rather than the ICK fold and will provide fundamental information for prediction algorithms, as the subtle complexity of disulfide isomers may be not adequately addressed by the current prediction algorithms.
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Affiliation(s)
- Tiziano Raffaelli
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia
| | - David T Wilson
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia
| | | | | | - Irina Vetter
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia; School of Pharmacy, The University of Queensland, Queensland, Australia
| | - Samuel D Robinson
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Ashvriya Thapa
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia; School of Pharmacy, The University of Queensland, Queensland, Australia
| | - Antin Widi
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia
| | - Alex Loukas
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia
| | - Norelle L Daly
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia.
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Bowhay CR, Hanington PC. Animal granulins: In the GRN scheme of things. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 152:105115. [PMID: 38101714 DOI: 10.1016/j.dci.2023.105115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/06/2023] [Accepted: 12/10/2023] [Indexed: 12/17/2023]
Abstract
Granulins are conserved in nearly all metazoans, with an intriguing loss in insects. These pleiotropic peptides are involved in numerous physiological and pathological processes yet have been overwhelmingly examined in mammalian systems. While work in other animal models has been informative, a richer understanding of the proteins should be obtained by integrating knowledge from all available contexts. The main bodies of work described here include 1) the structure-function relationships of progranulin and its cleavage products, 2) the role of expanded granulin gene families and different isoforms in fish immunology, 3) the release of granulin peptides to promote host angiogenesis by parasitic worms, 4) a diversity of molluscan uses for granulins, including immune activation in intermediate hosts to trematodes, 5) knowledge gained on lysosomal functions from C. elegans and the stress-related activities of granulins. We provide an overview of functional reports across the Metazoa to inform much-needed future research.
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Affiliation(s)
- Christina R Bowhay
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Patrick C Hanington
- School of Public Health, University of Alberta, Edmonton, AB, T6G 2R3, Canada.
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