Computational modelling of diatom silicic acid transporters predicts a conserved fold with implications for their function and evolution

Knight, M, Hardy, BJ, Wheeler, G and Curnow, P 2022 Computational modelling of diatom silicic acid transporters predicts a conserved fold with implications for their function and evolution. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1865 (1). https://doi.org/10.1016/j.bbamem.2022.184056

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Abstract/Summary

Diatoms are an important group of algae that can produce intricate silicified cell walls (frustules). The complex process of silicification involves a set of enigmatic integral membrane proteins that are thought to actively transport the soluble precursor of biosilica, dissolved silicic acid. Full-length silicic acid transporters are found widely across the diatoms while homologous shorter proteins have now been identified in a range of other organisms. It has been suggested that modern silicic acid transporters arose from the union of such partial sequences. Here, we present a computational study of the silicic acid transporters and related transporter-like sequences to help understand the structure, function and evolution of this class of membrane protein. The AlphaFold software predicts that all of the protein sequences studied here share a common fold in the membrane domain which is entirely different from the predicted folds of non-homologous silicic acid transporters from plants. Substrate docking reveals how conserved polar residues could interact with silicic acid at a central solvent-accessible binding site, consistent with an alternating access mechanism of transport. The structural conservation between these proteins supports a model where modern silicon transporters evolved from smaller ancestral proteins by gene fusion.

Item Type:	Publication - Article
Additional Keywords:	diatom silicic acid transporters, AlphaFold, computational models, substrate docking simulation
Subjects:	Marine Sciences
Divisions:	Marine Biological Association of the UK > Other (MBA)
Depositing User:	Ms Kristina Hixon
Date made live:	09 May 2023 09:42
Last Modified:	09 Feb 2024 16:57
URI:	https://plymsea.ac.uk/id/eprint/9894

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