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Biochemical and Structural Characterization of Helicobacter pylori Peptide deformylase by Computational Methods

Surekha Patil, Shivakumar B. Madagi


Helicobacter pylorus is classified as class one carcinogen in causing gastric cancer. Peptide deformylases (PDFs) present in bacteria removes the formyl group from the N-terminal Methionine of newly synthesized proteins which is necessary in protein maturation. These enzymes have shown as new targets in antibacterial, antimalarial and anticancer drug discovery. Here an insilico technique was initiated to characterize structural and biochemical properties of this protein. Pair wise sequence alignment with human PDF shows 31–47% identity, hence can be used as anticancer target in human. This enzyme is located in the cytoplasm of the cell, do not contain signal peptide, promiscuity site and vaccine targets. Physicochemical characterization is analyzed by Protparam tool reveals that this is an unstable protein, predicted Iso Electric Ph is 6.9 with total positively charged residues 29 and negatively charged residues 24. Conserved domain search shows one conserved domain and interacting partner from STRING search shows 10 interacting proteins. PDF is searched for MHC class-1 binding sites with 12 super types of MHC class-1 molecules has highest binding site of 8 and least binding site 1. Understanding of these characteristics of H. pylori peptide de-formulas may help in designing novel drugs to cure H. pylori caused infections.


Keywords: H. pylori, Peptide deformylases, computational tools, sequence alignment, conserved, Domain, epitopes


Cite this Article

Surekha Patil, Shivakumar B Madagi. Biochemical and Structural Characterization of Helicobacter pylori Peptide Deformylase by Computational Methods. Research & Reviews: A Journal of Bioinformatics. 2017; 4(3): 22–28p.


H.pylori, Peptide deformylase, computational tools, sequence alignment, conserved domain, epitopes

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