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Title: Translocation and interactions of L-arabinose in OmpF porin: A molecular dynamics study

Abstract

The passage of a natural substrate, L-arabinose (L-ARA) through Escherichia coli porin embedded in an artificial bilayer, is studied by equilibrium molecular dynamics simulations. We investigate the early stage of translocation process of L-ARA from intra-cellular to extra-cellular side (Int-to-Ext) across the bilayer. The average trajectory path over all L-ARA molecules along with quantum-mechanical configuration-optimizations at PM3 level predict the existence of at least three trapping zones. The common feature within all these zones is that L-ARA remains perpendicular to the channel axis. It is remarkable how the orientation and translational-rotational motion of L-ARA molecule play a role in its transport through OmpF channel. These simulations are important for better understanding of permeation process in OmpF channel. They also provide an insight into the chiral recognition of translocation process in protein nanochannels from substrate and protein prospects and help interpret experiments on permeation process of small dipolar molecules across biological membranes.

Authors:
 [1];  [2]
  1. Department of Chemistry, Tehran University, P.O. Box 14155-6455, Tehran (Iran, Islamic Republic of) and Schuit Institute of Catalysis, ST/SKA, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven (Netherlands). E-mail: K.Malek@tue.nl
  2. Department of Chemistry, Tehran University, P.O. Box 14155-6455, Tehran (Iran, Islamic Republic of)
Publication Date:
OSTI Identifier:
20857949
Resource Type:
Journal Article
Resource Relation:
Journal Name: Biochemical and Biophysical Research Communications; Journal Volume: 352; Journal Issue: 1; Other Information: DOI: 10.1016/j.bbrc.2006.10.183; PII: S0006-291X(06)02419-3; Copyright (c) 2006 Elsevier Science B.V., Amsterdam, The Netherlands, All rights reserved; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; ARABINOSE; CHIRALITY; CUBIC LATTICES; ESCHERICHIA COLI; MOLECULAR DYNAMICS METHOD; OPTIMIZATION; PROTEINS; SUBSTRATES; TRANSLOCATION

Citation Formats

Malek, Kourosh, and Maghari, Ali. Translocation and interactions of L-arabinose in OmpF porin: A molecular dynamics study. United States: N. p., 2007. Web. doi:10.1016/j.bbrc.2006.10.183.
Malek, Kourosh, & Maghari, Ali. Translocation and interactions of L-arabinose in OmpF porin: A molecular dynamics study. United States. doi:10.1016/j.bbrc.2006.10.183.
Malek, Kourosh, and Maghari, Ali. Fri . "Translocation and interactions of L-arabinose in OmpF porin: A molecular dynamics study". United States. doi:10.1016/j.bbrc.2006.10.183.
@article{osti_20857949,
title = {Translocation and interactions of L-arabinose in OmpF porin: A molecular dynamics study},
author = {Malek, Kourosh and Maghari, Ali},
abstractNote = {The passage of a natural substrate, L-arabinose (L-ARA) through Escherichia coli porin embedded in an artificial bilayer, is studied by equilibrium molecular dynamics simulations. We investigate the early stage of translocation process of L-ARA from intra-cellular to extra-cellular side (Int-to-Ext) across the bilayer. The average trajectory path over all L-ARA molecules along with quantum-mechanical configuration-optimizations at PM3 level predict the existence of at least three trapping zones. The common feature within all these zones is that L-ARA remains perpendicular to the channel axis. It is remarkable how the orientation and translational-rotational motion of L-ARA molecule play a role in its transport through OmpF channel. These simulations are important for better understanding of permeation process in OmpF channel. They also provide an insight into the chiral recognition of translocation process in protein nanochannels from substrate and protein prospects and help interpret experiments on permeation process of small dipolar molecules across biological membranes.},
doi = {10.1016/j.bbrc.2006.10.183},
journal = {Biochemical and Biophysical Research Communications},
number = 1,
volume = 352,
place = {United States},
year = {Fri Jan 05 00:00:00 EST 2007},
month = {Fri Jan 05 00:00:00 EST 2007}
}