Molecular dynamics study of prolyl oligopeptidase with inhibitor in binding cavity

Abstract

We used the crystal structure of prolyl oligopeptidase (POP) with bound Z-pro-prolinal (ZPP) inhibitor (Protein Data Bank (PDB) structure 1QFS) to perform an intensive molecular dynamics study of the POP-ZPP complex. We performed 100 ns of simulation with the hemiacetal bond, through which the ZPP is bound to the POP, removed in order to better investigate the binding cavity environment. From basic analysis, measuring the radius of gyration, root mean square deviation, solvent accessible surface area and definition of the secondary structure of protein, we determined that the protein structure is highly stable and maintains its structure over the entire simulation time. This demonstrates that such long time simulations can be performed without the protein structure losing stability. We found that water bridges and hydrogen bonds play a negligible role in binding the ZPP thus indicating the importance of the hemiacetal bond. The two domains of the protein are bound by a set of approximately 12 hydrogen bonds, specific to the particular POP protein.

Keywords:

• prolyl oligopeptidase
• POP
• molecular dynamics
• hydrogen bonds
• protein dynamics
• inhibitor ligands
• hemiacetal bond

Acknowledgements

This work was supported by the Natural Sciences and Engineering Research Council of Canada (M.K.) and the Academy of Finland (T.R.). Computational resources have been provided by SharcNet and the Finnish IT Centre for Science.