In Silico Prediction for the Binding Of AMPA-Receptor with Glutamate in Owl and Falcon

Abstract

The AMPA-receptor is a subtype of the ionotropic glutamate receptor that is linked to ion channels and can control cell excitability by gating calcium and sodium ions into the cell.This receptor affinity to bind with glutamate may be different between owl and falcon and affect their ability to transfer glutamate neurotransmitters to cells. This study was conducted to predict the biological affinity of both owl and falcon AMPA-receptors to bind with glutamate and to assess the possible consequences of this binding on the vision strength in both birds.AMPA-receptor 4 isoform-X1 primary structures of both owl and falcon were retrieved from NCBI. Both amino acid sequences were compared to find out the ratio of homologous sequences. Subsequently, 3D structures were generated for both proteins and superimposed to assess the ratio of homologous domains. Molecular docking reactions were performed between both AMPA-receptors with glutamate to assess the strength and mode of interaction between this ligand and both proteins. Root mean square fluctuations (RMSF) for both docked complexes were conducted to compare the stability of each receptor upon being docked with glutamate.it was shown that both investigated receptors hared considerable similarity in their amino acid sequences as only a few differences were found. 3D impositions showed a relatively low level of differences between both proteins. Molecular docking reactions showed that such differences were sufficient to induce considerable differences in docking strength and patterns of interaction between glutamate and these receptors. Glutamate was bound with owl AMPA-receptor with a higher docking score (-5.0 kcal/mol) than that found in the docked AMPA-receptor/glutamate complex (-4.3 kcal/mol). These results were confirmed by RMSF values that showed more fluctuations of flacon AMPA-receptor complex than that found in owl AMPA-receptor complex.our study showed that owl AMPA-receptor can bind with glutamate with more efficiency compared with falcon AMPA-receptor whether in terms of the strength and mode of binding. This higher affinity induces better transmission to glutamate throughout the cell membranes. Accordingly, owls may exhibit a better vision than that found in falcons. Further in vitro studies are suggested to provide a more in-depth interpretation for this finding.