A Comparative Analysis of Cockroach and Mosquito, Octopamine Receptor Homologues Produced Using Chimera, Swiss-Model,...

Homology modeling can help bridge the gap between missing 3D structures and available primary sequences of protein. More environmentally friendlier insecticides against domestic nuisance can target the octopamine receptor proteins, only expressed in invertebrates. Herein, octopamine receptor homologues from Periplaneta americana and Culex quinquefasciatus, which do not have tertiary structures in the Protein Data Bank (PDB), were built using homology modeling and evaluated with various molecular modeling tools. AlphaFold models (AFM), which use artificial intelligence from DeepMind, showed structural validity when superimposed on Swiss-Model models (SMM) for both insect octopamine receptor species. The UCSF Chimera and Modeler models (CMM) did not match those by AlphaFold and Swiss-Model irrespective of the insect species receptor model compared. The greatest discrepancy between any two structures resulted between AFM and CMM with only 21.46% similarity and 14.92% similarity between backbone αCs of their superimposed 3D structures, respectively, for cockroach and mosquito, yet their primary sequences are highly identical. The highest sequence identity for superimposed 3D structures occurred between AFM and SMM of cockroach at 75%, and their corresponding mosquito sequence at 35.12% just surpassed the threshold of pairwise structural validity set above 30%. The local model quality obtained from ProSA web server ranks AFM above SMM and CMM in that order, even though all models had good z-scores. Ramachandran plot paints a different picture where the CMM have a higher percentage of residues in the accepted zone and AFM have a few residues in the wrong places. However, the data from VADAR statistics show that AFM models are more thermodynamically stable with lower fraction of buried amino acids or charges. Docking studies conducted on UCSF Chimera software showed similarity in active site residues for AFM and SMM involved in a number of electrostatic and hydrophobic interactions. These include residues GLU202, LEU102, ASP95, and ASP105 for cockroach models and residues VAL24 and LEU174 for mosquito models. The active site of all protein models contains some identical residues found in bound complexes including GLU, LEU, APS, and SER, which happen to be in different positions. ANOVA analysis revealed no significant difference in docking energies, an indication that even when active site residues are different, they still conserve the essential qualities needed for binding. Thus, despite the differences in structures, based on validation evaluation, such differences are unlikely to affect binding with octopamine. However, for studies where the quaternary structure of a protein is crucial, the AFM that preserves the full quaternary structure is recommendable.