The results evaluated are in good agreement with available experimental data, thus providing detailed molecular models which can explain the structural and specificities differences between both zinc peptidases. Secondary structure calculations using DSSP method reveals the folding of R145/R723 residue of ECE-1/XCE into β-sheet structure while unfolding of the S2’ subsite residues in aECE-1 and sustained compact folding of that of aXCE. Molecular dynamics (MD) simulations identified the flexible transitions of F149/I150, N566/N571, W714/W719, and R145/R723 residues of ECE-1/XCE for the strong binding of the inhibitor. Homology model of XCE explained the role of non-conserved residues of its S2’ subsite. Molecular dynamics simulation of both enzymes was performed to analyze the dynamic nature of their active site residues in the absence and presence of the inhibitor. Phosphoramidon was docked into the binding site of XCE whereas phosphate oxygen of the inhibitor was used as water molecule to design the apo forms of both enzymes. To explore the structural differences between XCE and ECE-1, homology model of XCE was built using the complex structure of ECE-1 with phosphoramidon (pdb-id: 3DWB) as template.
In contrast, it’s well characterized homologue endothelin-converting enzyme-1 (ECE-1) showed broad substrate specificity and acts as endopeptidase as well as dipeptidase. X-converting enzyme (XCE) involved in nervous control of respiration, is a member of the M13 family of zinc peptidases, for which no natural substrate has been identified yet.
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