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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}
}
  • The OmpF porin from the Escherichia coli outer membrane folds into a trimer of {beta}-barrels, each forming a wide aqueous pore allowing the passage of ions and small solutes. A long loop (L3) carrying multiple acidic residues folds into the {beta}-barrel pore to form a narrow 'constriction zone'. A strong and highly conserved charge asymmetry is observed at the constriction zone, with multiple basic residues attached to the wall of the {beta}-barrel (Lys16, Arg42, Arg82 and Arg132) on one side, and multiple acidic residues of L3 (Asp107, Asp113, Glu117, Asp121, Asp126, Asp127) on the other side. Several computational studies havemore » suggested that a strong transverse electric field could exist at the constriction zone as a result of such charge asymmetry, giving rise to separate permeation pathways for cations and anions. To examine this question, OmpF was expressed, purified and crystallized in the P63 space group and two different data sets were obtained at 2.6 {angstrom} and 3.0 {angstrom} resolution with K{sup +} and Rb{sup +}, respectively. The Rb{sup +}-soaked crystals were collected at the rubidium anomalous wavelength of 0.8149 {angstrom} and cation positions were determined. A PEG molecule was observed in the pore region for both the K{sup +} and Rb{sup +}-soaked crystals, where it interacts with loop L3. The results reveal the separate pathways of anions and cations across the constriction zone of the OmpF pore.« less
  • The OmpF porin in the Escherichia coli outer membrane (OM) is required for the cytotoxic action of group A colicins, which are proposed to insert their translocation and active domains through OmpF pores. A crystal structure was sought of OmpF with an inserted colicin segment. A 1.6 {angstrom} OmpF structure, obtained from crystals formed in 1 M Mg{sup 2+}, has one Mg{sup 2+} bound in the selectivity filter between Asp113 and Glu117 of loop 3. Co-crystallization of OmpF with the unfolded 83 residue glycine-rich N-terminal segment of colicin E3 (T83) that occludes OmpF ion channels yielded a 3.0 {angstrom} structuremore » with inserted T83, which was obtained without Mg{sup 2+} as was T83 binding to OmpF. The incremental electron density could be modelled as an extended poly-glycine peptide of at least seven residues. It overlapped the Mg{sup 2+} binding site obtained without T83, explaining the absence of peptide binding in the presence of Mg{sup 2+}. Involvement of OmpF in colicin passage through the OM was further documented by immuno-extraction of an OM complex, the colicin translocon, consisting of colicin E3, BtuB and OmpF.« less