Bt Research 2025, Vol.16, No.4, 136-146 http://microbescipublisher.com/index.php/bt 143 Research has used AutoDock to simulate the binding of Cry1Ab toxin to the Cadherin receptor of the bollworm, identifying the EC repeat region of the surface loop region of the second domain of the toxin, and predicting key amino acid interactions (Hu et al., 2018). In some studies, AlphaFold predicted the interaction of the artificial polypeptide Bt Cry-GXJG-11 with the Cadherin receptor fragment of the bollworm. It was found that the two can form a stable complex and locate a key action site Tyr244. This is consistent with experimental evidence, demonstrating that this site is essential for toxin-receptor binding. In addition to receptor proteins, docking tools can also be used to screen for toxin inhibitors or additive molecules. Yang Xiaoyan et al. constructed a fusion protein by fusing two toxins with different receptor targeting properties (Cry1A.301 and Vip3A), and it was found that its activity against a variety of pests was significantly improved (Ahmad et al., 2015). This type of fusion strategy can also be designed with the help of molecular docking to ensure that both active domains can effectively approach their respective receptors in spatial structure. Figure 2 Tetrameric ‘membrane-inserted’ model of Cry1Aa domain I: (A–C) AF2-predicted tetrameric structure of domain I: side (A), top (B) and HOLE profile view (C); (A) helices 6 and 7 of one monomer were deleted for clarity; (D,E) helix α4 residues lining the channel in Cry1Aa (D) and Cry28Aa (E) in two opposed helices. Two monomers have been removed for clarity (Adopted from Torres et al., 2023) 7.3 Protein function annotation and GO/KEGG enrichment analysis In addition to the toxins themselves, a large number of other proteins encoded by the Bt genome are also worthy of attention, such as virulence-related enzymes, anti-resistance proteins, etc. Bioinformatics provides a variety of protein function annotation and enrichment analysis tools that can be used to predict the biological role of these proteins. One of the commonly used protein function annotation methods is sequence-based homologous search, such as using Blast to align Bt protein sequences to UniProt or NR databases to obtain possible functional domain information. Pfam database scans can also discover known functional domains in sequences, thereby inferring protein properties. For example, by GO classification of the whole protein collection of a Bt strain, it can be found that the proteins related to extracellular secretion and catabolism account for a high proportion of proteins in its proteome, which is consistent with the life history of Bt as a saprophytic/pathogenic bacteria that requires the secretion of multiple enzymes to degrade host tissues (Lavezzo et al., 2016). KEGG annotation can map Bt protein to metabolic pathway map, such as Bt has a complete tetrahydrofolate synthesis pathway, urea circulation pathway, etc., thereby speculating its ability in environmental nutrient utilization (Jong et al., 2022). 8 Data Integration and Visualization Platform 8.1 Bioinformatics data integration platform In recent years, some platform tools have emerged for integrating multi-omics data. For example, Galaxy's open scientific research platform allows researchers to connect different analysis tools into a workflow to uniformly process Bt's genome, transcriptome, and metabolomic data without the need to install complex software locally.
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