3.3. Construction of Homology-Based Tertiary Protein Structure

Homology-based protein tertiary structures (PDB files) of all the Betula AQPs were predicted using the Phyre2 protein-modeling server (http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index; accessed on 2 July 2021) [152], using the intensive modelling mode as parameter. The results obtained in the form of PDB files were then uploaded to the Mole2.5 server to predict the transmembrane pores and various biochemical properties of the pore-lining residues (https://mole.upol.cz/; accessed on 2 July 2021) [153]. The following default parameters were also used: heteroatoms were ignored for modelization and pore merging was set on. Channel modelization was obtained with cavity probe radius, 5 Å; cavity interior threshold, 1.1 Å; channel origin radius, 5 Å; channel surface cover radius, 5 Å; channel weight function, the Vororoi scale; bottleneck radius, 1.2 Å; bottleneck tolerance, 3 Å; and maximum tunnel similarity, 0.7 Å.