Homology Modeling of Coagulase in Staphylococcus aureus

Abstract

The close correlation between the ability of coagulase to clot blood plasma and their capacity to produce disease, and the corresponding absence of this property in nonpathogenic strains, have led to the assumption that the coagulase, plays important role in the pathogenesis of disease. Currently, crystal structure of coagulase in Staphylococcus aureus remains indefinable. Thus, the objectives of this research is to generate the three dimensional model of coagulase in S. aureus by using homology modeling approach. In this study, we used bioinformatics tools and databases such as BLAST (Basic Local Alignment Search Tool), GenBank, PDB (Protein Databank), and Discovery Studio to gain specific functional insights into coagulase. The model was validated using protein structure checking tools such as PROCHECK, Verify 3D and CE (Combinatorial Extension) for reliability. Therefore, structure prediction of coagulase in S. aureus can provide preliminary knowledge for understanding the function of the protein. The information from this finding will provide important information into the action and regulation mechanism of the coagulase protein in S. aureus.

Keywords: Staphylococcus aureus; Structure prediction; coagulase; homology modeling.

Figure 1

(a) Structural-based alignment of coagulase from S. aureus and the template PDB ID: 1NU9 (Staphylocoagulase- Prethrombin-2 complex). The sequence shaded in cyan represents sequence similarity; (b) The best predicted model of coagulase (coagulase.B99990002); (c) Ramachandran Plot of the coagulase model calculated by PROCHECK; (d) Superposition of the predicted model of coagulase from S. aureus onto to the template PDB ID: 1NU9.