alphafold2-multimer  (Thermo Fisher)

Journal: Communications Chemistry

Article Title: Human O- GlcNAcase catalytic-stalk dimer anchors flexible histone binding domains

doi: 10.1038/s42004-025-01813-7

Figure Lengend Snippet: Potential binding sites of the pHAT domains to nucleosomes, highlighting proximity and spacing of the H3K36 residues ( a ) as well as the H3K36 and H4K 5,8,12, and 16 residues ( b ) in the nucleosome (PDBID:1kx5: gray). OGA is colored by domain: catalytic domain, dark blue; stalk, yellow; linker, and HAT-like domain: green. The distance between K36 residues (red) is 73.5 Å, and the total distance between pHAT densities is 107 Å (green). The distance between the K36 residue and the H4K 5,8,12,16 is 72.8 Å (pink). c OGA-L pHAT binding to histone modifications such as H3K36 Me and acetylated H4 tails would facilitate recruitment to sites of active transcription and DNA repair. The structural features identified for OGA-L are likely to increase the local concentration of tihe OGA-L and allow flexible movement of the catalytic domain to facilitate O- GlcNAc removal from proteins in proximity. The OGA model is shown with unstructured linkers added from the Alphafold2 colored by domain: catalytic domain, dark blue; stalk, yellow; linker, and pHAT domain, green.

Article Snippet: Additional data compared in this study from the protein databank: Alphafold2 Multimer, PDB ID: 5M7R, PDB ID: 5VVO, PDB ID:5UHK, PDB ID: 5M7S, PDBID:5UN9, PDB ID:5UHL, PDB ID: 5M7T, PDB ID: 5UHO, PDB ID: 8P0L, PDB ID: 9BA8, 9BA9, PDB ID: 1KX5 .

Techniques: Binding Assay, Residue, Concentration Assay

Journal: Cureus

Article Title: Interaction Between HAQ-STING Mutation and COPA: Protection Against COPA Syndrome

doi: 10.7759/cureus.82254

Figure Lengend Snippet: The plot provides a visual representation of how well the input sequence aligns with other related sequences across the entire sequence. Except at positions 500 and 1220, a significant portion of the protein has moderate sequence identity. AF2M: AlphaFold2 Multimer

Article Snippet: In the current study, AlphaFold2 Multimer (AF2M) version 3 (DeepMind, London, UK) was used to assess the interaction between the COPA, STING, and HAQ-STING proteins.

Techniques: Sequencing

Journal: Cureus

Article Title: Interaction Between HAQ-STING Mutation and COPA: Protection Against COPA Syndrome

doi: 10.7759/cureus.82254

Figure Lengend Snippet: PAE plots assess structural confidence and domain flexibility. Blue (low PAE) indicates high-confidence intra-domain folding; red (high PAE) shows uncertain inter-domain positioning. Diagonal blue regions confirm well-defined COPA and HAQ-STING domains. Off-diagonal red regions reflect flexible or variable inter-domain orientations. Model 1 (rank_1) shows slightly higher structural definition. PAE: Predicted aligned error; AF2M: AlphaFold2 Multimer; STING: Stimulator of interferon genes

Article Snippet: In the current study, AlphaFold2 Multimer (AF2M) version 3 (DeepMind, London, UK) was used to assess the interaction between the COPA, STING, and HAQ-STING proteins.

Techniques:

Journal: Cureus

Article Title: Interaction Between HAQ-STING Mutation and COPA: Protection Against COPA Syndrome

doi: 10.7759/cureus.82254

Figure Lengend Snippet: pIDDT scores indicate high local structure confidence (70–90) for most residues, with dips below 50 marking flexible or disordered regions. A black line at position 1220 highlights a domain boundary or interaction site with notable structural variability. pIDDT: Predicted intrinsic distance difference test; AF2M: AlphaFold2 Multimer

Article Snippet: In the current study, AlphaFold2 Multimer (AF2M) version 3 (DeepMind, London, UK) was used to assess the interaction between the COPA, STING, and HAQ-STING proteins.

Techniques: