Homology Modeling of Plant Peptide Signals

Homology models of N-terminal truncated peptides signals of Amborella trichopoda (ATR0564G112-α; 129 aa, ATR0789G151-β; 118 aa), Arabidopsis thaliana (AT2G06925-α; 128 aa, AT2G19690-β; 119 aa), and Nicotiana tabacum TN90 (Gene_60450(SS4740)-α; 127 aa, Gene_37244 (SS1768)-β; 117 aa) were obtained through AlphaFold server and also predicted using Robetta server (https://robetta.bakerlab.org/), and RaptorX server (http://raptorx.uchicago.edu/). Moreover, homology models of C-terminal regions (containing PA2c domain) of PLA2-like sequences were predicted for Amborella trichopoda (AmTr _scaffold00063; 168 aa), Arabidopsis thaliana (AT4G29070- 145 aa), and Nicotiana tobacumTN90 (mRNA_158062; 149 aa). For Robetta and RaptorX, five models of each protein were generated, and the model qualities were compared with the AlphaFold predictions using the SWISS-refinement server (https://swissmodel.expasy.org/assess). MolProbity Score, clash score, Ramachandran scores, and QMEAN were considered to select the best model among all generated predictions. Further, electrostatic potentials for the best models were calculated using APBS web-server (Adaptive Poisson-Boltzmann Solver, https://www.poissonboltzmann.org/) and plotted on the predicted protein structures (Unni et al., 2011 (link)). The conserved residues and non-conserved residues were analyzed using the Consurf web-server (https://consurf.tau.ac.il/) for the best models. All the generated models were visualized and edited using the CHIMERA (https://www.cgl.ucsf.edu/chimera/).