Fig 1.
a) MCTP4 TMR having 5 elements: 2 transmembrane hairpins (HP1 and HP2) and 3 amphipathic helices (AH1, TM0 and AH2).
b) AF MCTP4 model oriented in the lipid bilayer by OPM server [30].
Table 1.
RMSD values for the transmembrane domain (550-776) (upper half) and for the alpha carbon of entire models (lower half). For each pair of models, the RMSD value is indicated for each measurement.
Fig 2.
Evaluation of model predictions using the pLDDT score as a function of residues in the HP1 (left) and HP2 (right) regions.
The curves of different colors represent models predicted by various prediction methods: AlphaFold (AF, red), OmegaFold (OF, blue), TR (green), ESM (yellow), and AlphaFold Multimer (AFM, magenta).
Fig 3.
Contact maps between the residues of transmembrane HP1 and HP2 of different protein structures: a) ESM, b) AFM, c) AF, d) TR, e) RF and f) OF.
The distances were calculated using the alpha carbon atoms. Heat map coloring indicates the distance between residues, ranging from dark purple for short distances to white for longer distances(12 A). g) superposition of ESM, AFM, TR and RF transmembrane domain models. h) and j) are OF and AF transmembrane domains.
Fig 4.
a) AlphaFold multimer prediction of TMR MCTP4 protein.
The HP1 domain is represented in orange and the HP2 domain in purple. The pLDDT score between residues of interchain domains is represented by lines, with the blue color indicating a high score. b) Predicted Aligned Error (PAE) for the MCTP4 dimer, extracted by AlphaPickle [34]. PAE provides an estimate of the error in the predicted alignment of residues. c) Inter-chain contact map of TMR. d) Close-up view of the PAE for the TMR of MCTP4.
Fig 5.
Principal Component Analysis (PCA) plots, clustering and density representation.
a) The plot shows a projection based on a PCA’s first two principal components (PCs). Large points represent the starting points of each simulation for each model, and small points are conformations generated by the simulation in each model. Each model is represented by its own colour: AlphaFold (AF, red), OmegaFold (OF, blue), TR-rosetta (TR, green), ESMFold (ESM, yellow), AlphaFold Multimer (AFM, magenta), AlphaFold v3 (AF3, dark red) , Boltz-1 (Boltz, light purple) and Chai-1 (Chai, light pink). b) The centroids of each basin have been determined using the K-medoid clustering method. c) A density plot showing the projection of the two PCs, where each point corresponds to the starting point of each model. d) The representative structure of each cluster is shown with a contact map corresponding to contacts between transmembrane domains.