Molecular docking of Enterocin-P peptide with DNA: an in silico study

Antibiotic resistance is a looming public health crisis especially in animal industry. Hence, researchers arelooking for natural alternatives such as Antimicrobial peptides (AMPs). Nowadays, AMPs, also known ashost defense peptides, are short and generally positively charged peptides found in a wide variety of lifeforms from microorganisms to humans. One of the modes of action of some AMPs were the binding withDNA and can directly affect the expression of related genes and inhibit the synthesis of macromolecules ordestroy. Among AMPs Entrocin-P peptide has attracted a lot of attention from researchers. The aim of thisstudy was to evaluated the possibility of binding DNA to Entrocin-P peptide. The structure of Entrocin-ppeptide was obtained from previous study. A general strategy for docking and modelling DNA–proteincomplexes has been developed with HADDOCK server. HADDOCK uses non-structural experimental datato drive the docking during a rigid-body energy minimization, and semi-flexible and water refinement stages.The latter allow for flexibility of all DNA nucleotides and the residues of the protein at the predicted interface.Using this method, we have reproduced the structure of Entrocin-P peptide bound to DNA. The results haveshown that the model of the Entrocin-P -DNA complex successfully has predicted. Furthermore, the resultsindicated that interactions were occurred by the major groove of DNA with α-helix part of this peptide. Thebest haddock score was -۷۴.۳ +/- ۳.۵. In addition, the value of Z-Score was -۲.۵. Its Z-score indicates howmany standard deviations from the average this cluster is located in terms of score that the more negative thebetter.

کلیدواژه ها:

Entrocin-P ، Peptide ، Bioinformatics ، DNA ، Molecular docking