Study of the defensive behavior of Iraqi honeybee’s colonies (order: hymenoptera) in Basra province – Iraq

Abstract

Computational methods were used to investigate both the physical and chemical properties of UDP-glucose 6-dehydrogenase (hUGDH). Secondary structure analysis of the query model was done using the Self-Optimized Prediction method With alignment (SOPMA), the secondary structure predictions comprise of 40.69% Alpha helixes (Hh), 17.61% Extended strand (Ee), 7.69% Beta turn (Tt) and 34.01% of Random coil (Cc) with aliphatic index of 90.00 and an instability index of 33.26 which classify the protein model to be thermally stable irrespective of it environment. Comparative modeling was used to predict a reliable tertiary structure for hUGDH and the obtained 3-dimensional model was validated using DOPE score profile, Ramachandran plot, and the QMEAN Z-score. The DOPE score profile shows a high similarity between the model and the template as little or no disparity was found in the profile patterns. Ramachandran plot of the model also shows that 92.5% of the amino acid residues were found at the most favored regions which make it stereo-chemically stable. The QMEAN z-score of UDP-glucose 6-dehydrogenase was predicted to be -0.15. The superimposed structure of the model and the template also gave RMSD of 0.125. All this shows that the predicted model is of good quality. An RMSD and Rg run via molecular dynamics (MD) simulation equally shows that the protein model attained stability at around 10ns. Protein – Protein interaction (PPI) network was also generated for the model with a high confidence score from UDP-glucuronic acid decarboxylase 1 (UXS1) when interacted with the other twenty proteins. In addition, the docking studies of the model and 3PRJ receptors with two prostate cancer drugs, i.e. Apalutamide and Darolutamide gave similar binding affinity ranging between 6.0kcal/mol – 8.0kcal/mol for the most favored binding of the two drugs. Hence, the model can serve as a molecular target for designing new inhibitors for prostate cancer.