The present study was conducted to design and analyze the structural model of buffalo pregnancy-associated glycoprotein-1 (PAG-1) using bioinformatics. Structural modeling of the deduced buffalo PAG-1 protein was done using PHYRE, CONSURF servers and its structure was subsequently constructed using MODELLER 9.9 and PyMOL softwares Buffalo PAG-1 structural conformity was analyzed using PROSA, WHATIF, and 3D-PSSM servers. Designed buffalo PAG-1 protein structure on BLAST analysis retrieved protein structures belonging to aspartic proteinase family. Moreover in silico analysis revealed buffalo PAG-1 protein retained bilobed structure with pepstatin-binding clefts near the active sites by docking studies with pepstatin A using PatchDock server. Structural studies revealed that the amino and carboxy terminal containing aspartic residues are highly conserved and buried within the protein structure. Structural conformity studies showed that more than 90% of the residues lie inside favored and allowed regions. It was also deduced that buffalo PAG-1 possesses low and high energy zones with a very low threshold for proteolysis ascertaining the stableness of the buffalo PAG-1 protein structure. This study depicts the structural conformity and stability of buffalo PAG-1 protein. 1. Introduction The pregnancy-associated glycoproteins (PAGs) constitute a large group of proteins belonging to the aspartic proteinase superfamily expressing in the placenta of eutherian mammals. PAGs are acidic glycoprotein sharing more than 50% amino acid sequence identities with Pepsin, Cathepsin D and E [1]. They are secreted from the outer epithelial cell layer of placenti of various ungulate species possessing a predominant role in the placentogenesis, placental modeling, and embryogenesis during pregnancy in domestic species. Many PAG genes have been cloned and identified in many domestic animals such as cattle, sheep, goat, pig, and wild ruminants’ species [2–4]. Structural modeling studies in bovine and porcine reveal their bilobed structure and proteolytically inactiveness due to key mutation at the active sites (alanine replaced by glycine: Gly34) residue whose presence would cause displacement of the catalytic water molecule from its normal position between the two catalytic aspartic residues (Asp32 and Asp215). Studies on bovine PAGs show that they have retained the peptide-binding cleft of aspartic proteinases to bind pepstatin and this property is an important factor to characterize members of aspartic proteinase. Moreover PAGs share their identity with other members of
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