Molecular docking vNAR T1/TGF-β isoforms or TGF-β/TGFβRII

A protein–protein docking protocol was performed to predict the potential binding site of the vNAR T1 to TGF-β isoforms using the ClusPro web tool (https://cluspro.bu.edu/)⁶⁸. The models were obtained with MODELLER v.9.16⁶³ and refined with NAMD with 50 ns of contact. The model with extended time in the dynamic in silico assay was selected as the most thermostable. The vNAR-TGF-β complex (all three isoforms) with good electrostatics and desolvation-free energies were selected. The protein–protein interaction regions were predicted using Peptiderive, located on the ROSIE server (https://rosie.graylab.jhu.edu/peptiderive/). Default settings and the plots with the predicted protein–protein interactions were ranked according to the Rosetta Energy Units (REU)^68,69. The server PDBePISA (http://www.ebi.ac.uk/pdbe/prot_int/pistart.html)⁶⁹ was used to individually analyze interfacing residues between hTGF-β1(PDB ID 1KLA), TGF-β2 (PDB ID 2TGI), TGF-β3 (PDB ID 1KLA) and the vNAR T1 or with TGF-βRII receptor (PDB ID 3KFD).