alphafold multimer v2 3 prediction  (Molecular Dynamics Inc)

Journal: bioRxiv

Article Title: Interactions of outer membrane lipoproteins P. aeruginosa PA3214 and E. coli PqiC with their MCE protein binding partners, PA3213 and PqiB

doi: 10.64898/2026.05.09.724024

Figure Lengend Snippet: A , schematic of the P. aeruginosa PA3211-PA3214 operon overexpression construct used for structural studies. B , consensus map (Map 4) of protein complex after affinity purification and size exclusion. Inset shows a slice through the side view and top view of the consensus map, in which density likely corresponding to the PA3213 MCE protein is observed inside the PA3214 lipoprotein pore. C , AlphaFold 3 prediction of the PA3211-PA3212-PA3213-PA3214 complex, with PA3214 fit into the consensus map (Map 4). D , Surface representation of the PA3214 structure after focused refinement (Map 2, Fig. S6), with C-terminal peptide of PA3213 shown as sticks. Boxed region shows the interaction between the C-terminal peptide of PA3213 and the hydrophobic groove of PA3214. E , top views of the PA3214 model in the closed and open conformations fit into the respective maps (Map 2, closed; Map 3, open). Each protomer is shown in a different color. F , examples of 2D classes representing likely compositional and conformational heterogeneity in PA3214 bound to PA3213.

Article Snippet: We utilized the AlphaFold 3 prediction software available on Google DeepMind’s AlphaFold Server ( ) ( https://alphafoldserver.com/ ) to make predictions for the PA3211-PA3214 complex and the PqiBC complex.

Techniques: Over Expression, Construct, Affinity Purification

Journal: bioRxiv

Article Title: Interactions of outer membrane lipoproteins P. aeruginosa PA3214 and E. coli PqiC with their MCE protein binding partners, PA3213 and PqiB

doi: 10.64898/2026.05.09.724024

Figure Lengend Snippet: A , cartoon representation PqiC octamer and surface representation of a monomer, where hydrophobic groove residues identified as important by DMS are depicted in green on both the octamer and the monomer. B , DMS data corresponding to the residues shown in A , as presented in . C , Alphafold 3 prediction of PqiC in complex with the C-terminal region of PqiB. Surface representation of the PqiC predicted model with C-terminal peptide of PqiB shown as sticks. Inset focuses on the predicted interaction between PqiB and PqiC, showing the C-terminal peptide of PqiB and surrounding regions in the hydrophobic groove of PqiC. D , representative Western blot from a pull-down assay to assess the interaction between PA3213 and PA3214. All four subunits of the PA3211-PA3214 complex were over-expressed, with a His tag on the PA3214 bait, and interaction with untagged PA3213 was assessed using an ⍺-PA3213 antibody. Blots showing the solubilized membrane fraction of each strain (input, expression control), and the results of the pull-down are shown. Three independent purifications were performed starting with three different inoculations, with similar results. E , representative Western blot from a pull-down assay to assess the interaction between PqiB and PqiC. All three subunits of the PqiABC complex were over-expressed, with a His tag on the PqiB bait, and interaction with untagged PqiC was assessed using an ⍺-PqiC antibody. Blots showing the solubilized membrane fraction of each strain (input, expression control), and the results of the pull-down are shown. Three independent purifications were performed starting with three different inoculations, with similar results.

Article Snippet: We utilized the AlphaFold 3 prediction software available on Google DeepMind’s AlphaFold Server ( ) ( https://alphafoldserver.com/ ) to make predictions for the PA3211-PA3214 complex and the PqiBC complex.

Techniques: Western Blot, Pull Down Assay, Membrane, Expressing, Control

Journal: Nature Metabolism

Article Title: iNOS modulates inflammatory responses in an NO-independent manner through direct interaction with IRG1 in mitochondria

doi: 10.1038/s42255-026-01492-1

Figure Lengend Snippet: a , AlphaFold Multimer v2.3 prediction of the IRG1-iNOS dimer (IRG1 monomer with iNOS monomer). b , Molecular dynamics simulations at different temperatures showing that the interaction between the units is stable. c , MM/GBSA free energy calculations of three snapshots of the molecular dynamics simulations.

Article Snippet: Extended Data Fig. 7 Computational modelling of the interaction between monomers of mouse IRG1 and iNOS. a , AlphaFold Multimer v2.3 prediction of the IRG1-iNOS dimer (IRG1 monomer with iNOS monomer). b , Molecular dynamics simulations at different temperatures showing that the interaction between the units is stable. c , MM/GBSA free energy calculations of three snapshots of the molecular dynamics simulations.

Techniques: