Journal: Proteomics

Article Title: Discriminating physiological from non-physiological interfaces in structures of protein complexes: a community-wide study

doi: 10.1002/pmic.202200323

Figure Lengend Snippet: Classification performance of AlphaFold2 models predicted for the physiological and non-physiological homo dimers of the benchmark dataset. This is evaluated on the subset of 1480 targets for which results were produced with all AlphaFold2 versions. Column 1 lists the version of AlphaFold used for the predictions, and the score used to quantify the similarity between the AlphaFold2 predicted model, and the homodimer structures of the corresponding benchmark entry (see Main text for detail). Column 2 lists the Area Under the Curve (AUC) of the ROCs computed using the listed scores. Columns 3 and 4 list the mean and median values for the computed scores considering only the physiological dimers. Those for the non-physiological dimers are not reported, as AlphaFold2 tends to predict alternative association modes for a significant fraction of these dimers, as expected.

Article Snippet: G.T., L.P., and T.S. acknowledge the contributions of Gabriel Studer in setting up the AlphaFold pipeline for our analysis, sciCORE at the University of Basel for providing computational resources and system administration support, and funding from the SIB Swiss Institute of Bioinformatics and the Biozentrum PhD Fellowships.

Techniques: Produced

Journal: bioRxiv

Article Title: Feather keratin in Pavo cristatus : A tentative structure

doi: 10.1101/2024.09.08.611866

Figure Lengend Snippet: AlphaFold prediction of most parsimonious tentative structure of the F-keratin tetrameric N-block, AA 1-–52 (4 × 52 = 208 residues). Monomers are color-coded by chain (blue, red, green, yellow). Cysteine residues are displayed in a ball-stick view with standard colors. (a) Side view, staircase arrangement of helical β -strands in levels 1-8 (highlighted in the colors of adjacent β -strands) in the axial direction. Chain orientations of individual monomers are indicated by the respective AA number. (b) side view 90° turned, β -strands are rotationally staggered by an average horizontal angle of 11.125°per β -strand. The 8th strand is rotated 89°against the 1st strand in Pavo cristatus . The distance between the sandwiched sheets is 1.0-1.2 nm. Note that the polypeptide backbones of the four monomers are intertwined between strands in levels 4 and 5. (c) Axial view. (d) Equatorial cross-section of (a), corresponding to (c). AA 37-S, 38-T, and 47-I sit in the equatorial plane.

Article Snippet: So far, according to AlphaFold models, C-block segments of Gallus gallus and Larus novaehollandiae lack such interfacial fit.

Techniques: Blocking Assay

Journal: bioRxiv

Article Title: Feather keratin in Pavo cristatus : A tentative structure

doi: 10.1101/2024.09.08.611866

Figure Lengend Snippet: AlphaFold prediction of the Pavo cristatus F-keratin tetrameric C-block, AA 81-–100 (4 × 20 = 80 residues). Monomers are color-coded by chain (blue, red, green, yellow). The four 98-Y and 12 cysteine residues are displayed in a ball-stick view with standard colors. Chain orientations of individual monomers are indicated by the respective amino acid number. (a) Side view, filament axis vertical. (b) The side view turned 90°around the filament axis. (c) Top view, along the filament axis. Note that each pair of β -strands forms one level; the arrangement is rectangular rather than square in the (x,y) plane. The direction of the β -strand arrows is from N-to C-terminus. (d) shows the outer aromates from the 81-FGYGFGGLGCF motif in the same view as (b).

Article Snippet: So far, according to AlphaFold models, C-block segments of Gallus gallus and Larus novaehollandiae lack such interfacial fit.

Techniques: Blocking Assay