Journal: bioRxiv
Article Title: Short linear motifs - Unexplored players driving Toxoplasma gondii infection
doi: 10.64898/2026.01.12.699020
Figure Lengend Snippet: A. Protein diagrams of RON6, RON10, GRA7 and GRA15 indicating the position of their TRAF6-binding motifs with accompanying multiple sequence alignment showing their presence in different Toxoplasma strains and Coccidian species. B. AlphaFold model of TRAF6 MATH domain with TRAF6-binding motif from RON10. Right panels display the potential hydrogen bond network at the interaction interface (top) and secondary structure adopted by the TRAF6-binding motif (bottom). C. RON10 TRAF6 motif testing. MST traces (top graph) and dose-response curves (bottom panel) of TRAF6 MATH domain binding to RON10 TRAF6 motif containing peptide (left) and the E>S mutant (right). In the MST traces, the cold region is set at 0 s (blue) and the hot detection region at 5 s (red). D . Same as in A, but for the GRA15 TRAF6 motif and the E>S motif mutant.
Article Snippet: The local installation of AlphaFold Multimer version 2.3.2 was run using the following parameters and following Alphafold GitHub instructions ( https://github.com/deepmind/alphafold#running-alphafold ): --model_preset=multimer \ --db_preset=full_dbs \ --max_template_date=2020-05-14 \ --num_multimer_predictions_per_model=1 \ --use_gpu_relax=True \ -- bfd_database_path=/mnt/storage/alphafold/v232/bfd/bfd_metaclust_clu_complete_id30_c90 _final_seq.sorted_opt \ --mgnify_database_path=/mnt/storage/alphafold/v232/mgnify/mgy_clusters_2022_05.fa \ --obsolete_pdbs_path=/mnt/storage/alphafold/v232/pdb_mmcif/obsolete.dat \ --pdb_seqres_database_path=/mnt/storage/alphafold/v232/pdb_seqres/pdb_seqres.txt \ --template_mmcif_dir=/mnt/storage/alphafold/v232/pdb_mmcif/mmcif_files \ --uniprot_database_path=/mnt/storage/alphafold/v232/uniprot/uniprot.fasta \ --uniref90_database_path=/mnt/storage/alphafold/v232/uniref90/uniref90.fasta \ --uniref30_database_path=/mnt/storage/alphafold/v232/uniref30/UniRef30_2021_03 \ --use_precomputed_msas=True
Techniques: Binding Assay, Sequencing, Mutagenesis
