Interaction of Antimicrobial Peptide Pardaxin with DPPC Bilayers by Molecular Dynamics Simulation

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DOUSTDAR F.; Aghdami r.; MEHRNEJAD F.; CHAPARZADEH N.

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Journal: JOURNAL OF BIOTECHNOLOGY Year:2018 | Volume:9 | Issue:1 Page(s): 17-22

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Title

Interaction of Antimicrobial Peptide Pardaxin with DPPC Bilayers by Molecular Dynamics Simulation

Author(s)

DOUSTDAR F. | Aghdami r. | MEHRNEJAD F. | CHAPARZADEH N. | Issue Writer Certificate

Keywords

PardaxinQ1

Molecular Dynamics SimulationQ1

Antimicrobial PeptideQ1

MembraneQ1

Abstract

Aims Today, due to the advent of drug resistance in cancer cells against conventional drugs, attention has been paid to the development of anti-cancer drugs with new mechanisms. Pardaxin is an amphipathic polypeptide neurotoxin. The aim of this study was to investigate the interaction of Antimicrobial Peptide Pardaxin with DPPC (composed of 1, 2-dipalmitoyl-snglycero-3-phosphocholine) bilayers by Molecular Dynamics Simulation. Materials & Methods In the present study, simulations for different Membrane environments were designed under neutral pH conditions. At first, the Linux system was used to install the VMD 1. 8. 6 (Visual Molecular Dynamics) software; then, Gromacs 4. 5. 5 software was used to perform all the simulations. The pdb peptide structure (1XC0) was prepared from the Protein Data Bank and DPPC lipid bilayer was used for lipid-peptide simulation. Findings During the 500 nanoseconds of simulation, the peptide was infiltrated into the Membrane. In the DPPC system, at first, the number of hydrogen bonds between the peptide and the lipid bilayer were increased and, then, remained almost constant until the end of the simulation and decreased over time with the number of hydrogen bonds between peptides and water. Pardaxin contacted with the Membrane surface and entered into the Membrane. In the presence of the peptide, the thickness of the Membrane and the range of each lipid decreased and the Membrane penetration increased. Conclusion The mechanism of Pardaxin is dependent on the bilayer composition, so that the Pardaxin peptide contacts with DPPC lipid Membrane surface and enters into it.

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APA: Copy

DOUSTDAR, F., Aghdami, r., MEHRNEJAD, F., & CHAPARZADEH, N.. (2018). Interaction of Antimicrobial Peptide Pardaxin with DPPC Bilayers by Molecular Dynamics Simulation. JOURNAL OF BIOTECHNOLOGY, 9(1 ), 17-22. SID. https://sid.ir/paper/231325/en

Vancouver: Copy

DOUSTDAR F., Aghdami r., MEHRNEJAD F., CHAPARZADEH N.. Interaction of Antimicrobial Peptide Pardaxin with DPPC Bilayers by Molecular Dynamics Simulation. JOURNAL OF BIOTECHNOLOGY[Internet]. 2018;9(1 ):17-22. Available from: https://sid.ir/paper/231325/en

IEEE: Copy

F. DOUSTDAR, r. Aghdami, F. MEHRNEJAD, and N. CHAPARZADEH, “Interaction of Antimicrobial Peptide Pardaxin with DPPC Bilayers by Molecular Dynamics Simulation,” JOURNAL OF BIOTECHNOLOGY, vol. 9, no. 1 , pp. 17–22, 2018, [Online]. Available: https://sid.ir/paper/231325/en

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