Volume 10, Issue 1 (2019)                   JMBS 2019, 10(1): 93-101 | Back to browse issues page

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Poulakchi Saber S, Arab S. Molecular Dynamic Simulations of OmpF in a Double Bilayer Membranes: The Different Behavior of OmpF in an asymmetric Ionic Concentration System. JMBS 2019; 10 (1) :93-101
URL: http://biot.modares.ac.ir/article-22-14437-en.html
Molecular Dynamic Simulations of OmpF in a Double Bilayer Membranes: The Different Behavior of OmpF in an asymmetric Ionic Concentration System
S. Poulakchi Saber1 , S.Sh. Arab * 2
1- Biophysics Department, Biological Sciences Faculty, Tarbiat Modares University, Tehran, Iran
2- Biophysics Department, Biological Sciences Faculty, Tarbiat Modares University, Tehran, Iran, Biophysics Department, Biological Sciences Faculty, Tarbiat Modares University, Nasr Bridge, Jalal-Al-Ahmad Highway, Tehran, Iran , sh.arab@modares.ac.ir
Abstract:   (6378 Views)
OmpF is one of the bacterial outer membrane protein which can transfer the ions into the membrane. During the last years different theoretical and experimental methods have been used for the investigation of the bacterial protein. In this study for retaining periodic boundary condition and investigation of the channel structural changes, we use double lipid bilayer in the system. Different ion concentration was applied into the lipid bilayers to make simulation much more realistic. The aim of this simulation is if there is any prominent direction in the ion passage of the channels. Structural analysis for two proteins with a different orientation is dissimilar and dssp analysis shows different peaks although there are common peaks. Lining residues and constriction zone amino acids in the two final frames are also diverse. There is no ion passage thorough protein 2. The results are completely different for the ion channels and it shows which after 100ns simulation one of the channels which its direction is similar to the natural channel in the bacterial membrane is open and the ion passage is clear and the other channel is completely closed which is related to the direction of the channel due to the ion concentration.
Keywords: Double Bilayer Simulation, Membrane Protein Simulation, Asymmetric Ion Concentration, OmpF
Full-Text [PDF 1572 kb]   (2576 Downloads)    
Subject: Agricultural Biotechnology
Received: 2017/06/9 | Accepted: 2017/09/6 | Published: 2019/03/16
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