Date of Award


Degree Type


Degree Name

Master of Science


Applied Mathematics


Prof. M. Karttunen


Prolyl Oligopeptidase (POP), a member of the prolyl endopeptidase family, has a role in several neurological disorders. Its primary function is to cleave an oligopeptidase, including neuroactive peptides. On the other hand POP with a Z-Pro-prolinal (ZPP) inhibitor may revert memory loss from neurological disorders, amnesic agents and aging. Here, the crystal structure of POP protein with ZPP inhibitor (Protein Data Bank PDB) and without ZPP inhibitor is studied using classical molecular dynamics simulations and the POP-ZPP complex behaviour is compared with pure POP. The basic analysis of the structures, included measuring radius of gyration and root mean square deviation which proved that POP structure with non-bonded ZPP and without ZPP are stable and maintain their structure over the entire simulation time. Moreover, principal component analysis (PCA) is used to analyze the motions of the structures by extracting the normal modes of motions in POP with and without presence of ZPP inhibitor.



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