Computational approaches on the Conjugation of a biogenic polyamine with a model enzyme (Proteinase K)

Computational approaches on the Conjugation of a biogenic polyamine with a model enzyme (Proteinase K)
Mansoore Hosseini-Koupaei,^1,* Yousof Bavafa,²
1. Assistant Professor of Biochemistry, Department of Biology, Faculty of Science, Naghshejahan Higher Education Institute. Isfahan. Iran
2. Department of Biology, Faculty of Science, Naghshejahan Higher Education Institute. Isfahan. Iran
Introduction: In order to understand the influence of polyamines on proteins, we used bioinformatics simulation methods including molecular dynamic simulation and ducking methods on the interaction of proteinase K (PK) as a model enzyme combined with spermine (as a polyamine).
Methods: Molecular docking is one of the best theoretical methods to investigate the correct binding site of small ligands (such as polyamines) on enzyme or protein. Molecular dynamic (MD) simulation is a powerful tool to investigate the protein alterations in the presence of ligand over a define time scale
Results: The molecular simulation results demonstrated that spermine could spontaneously bind and alter the structure of PK. Overall; the results showed that spermine could bind to PK and improve its stability and activity, thereby promising various biotechnological and industrial applications. Molecular dynamic studies showed that spermine acted as a stabilizer. The molecular docking results showed that the combination process is spontaneous (negative value of ∆G◦).
Conclusion: These results are is in agreement with experimental results, and also revealed that spermine was especially on the surface of the enzyme with different hydrogen and hydrophobic interactions and stable PK as model enzyme
Keywords: Bioinformatics insights, Proteinase K (PK), polyamine, Molecular dynamic and ducking simulations