help button home button Biophys. J.
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Tieleman, D. P.
Right arrow Articles by Berendsen, H. J. C.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Tieleman, D. P.
Right arrow Articles by Berendsen, H. J. C.

Biophys J, June 1998, p. 2786-2801, Vol. 74, No. 6

A Molecular Dynamics Study of the Pores Formed by Escherichia coli OmpF Porin in a Fully Hydrated Palmitoyloleoylphosphatidylcholine Bilayer

D. P. Tieleman and H. J. C. Berendsen

BIOSON Research Institute and Laboratory of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands

In this paper we study the properties of pores formed by OmpF porin from Escherichia coli, based on a molecular dynamics simulation of the OmpF trimer, 318 palmitoyl-oleoyl-phosphatidylethanolamine lipids, 27 Na+ ions, and 12,992 water molecules. After equilibration and a nanosecond production run, the OmpF trimer exhibits a C-alpha root mean square deviation from the crystal structure of 0.23 nm and a stable secondary structure. No evidence is found for large-scale motions of the L3 loop. We investigate the pore dimensions, conductance, and the properties of water inside the pore. This water forms a complicated pattern, even when averaged over 1 ns of simulation time. Around the pore constriction zone the water dipoles are highly structured in the plane of the membrane, oriented by the strong transversal electric field. In addition, there is a net orientation along the pore axis pointing from the extracellular to the intracellular side of the bilayer. The diffusion coefficients of water inside the pore are greatly reduced compared to bulk. We compare our results to results from model pores (Breed et al., 1996. Biophys. J. 70:1643-1661; Sansom et al. 1997. Biophys. J. 73:2404-2415) and discuss implications for further theoretical work.

Biophys J, June 1998, p. 2786-2801, Vol. 74, No. 6
© 1998 by the Biophysical Society   0006-3495/98/06/2786/16  $2.00


This article has been cited by other articles:


Home page
 Biophys. JHome page
R. A. Bockmann, B. L. de Groot, S. Kakorin, E. Neumann, and H. Grubmuller
Kinetics, Statistics, and Energetics of Lipid Membrane Electroporation Studied by Molecular Dynamics Simulations
Biophys. J., August 15, 2008; 95(4): 1837 - 1850.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
J. Jeon and G. A. Voth
Gating of the Mechanosensitive Channel Protein MscL: The Interplay of Membrane and Protein
Biophys. J., May 1, 2008; 94(9): 3497 - 3511.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
S. Leekumjorn, Y. Wu, A. K. Sum, and C. Chan
Experimental and Computational Studies Investigating Trehalose Protection of HepG2 Cells from Palmitate-Induced Toxicity
Biophys. J., April 1, 2008; 94(7): 2869 - 2883.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
W. Fu, J. Shen, X. Luo, W. Zhu, J. Cheng, K. Yu, J. M. Briggs, G. Jin, K. Chen, and H. Jiang
Dopamine D1 Receptor Agonist and D2 Receptor Antagonist Effects of the Natural Product ( ) Stepholidine: Molecular Modeling and Dynamics Simulations
Biophys. J., September 1, 2007; 93(5): 1431 - 1441.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
J. Aittoniemi, P. S. Niemela, M. T. Hyvonen, M. Karttunen, and I. Vattulainen
Insight into the Putative Specific Interactions between Cholesterol, Sphingomyelin, and Palmitoyl-Oleoyl Phosphatidylcholine
Biophys. J., February 15, 2007; 92(4): 1125 - 1137.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
S. Y. Bhide, Z. Zhang, and M. L. Berkowitz
Molecular Dynamics Simulations of SOPS and Sphingomyelin Bilayers Containing Cholesterol
Biophys. J., February 15, 2007; 92(4): 1284 - 1295.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
T. P. Nygaard, C. Rovira, G. H. Peters, and M. O. Jensen
Ammonium Recruitment and Ammonia Transport by E. coli Ammonia Channel AmtB
Biophys. J., December 15, 2006; 91(12): 4401 - 4412.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
D. Y. Haubertin, H. Madaoui, A. Sanson, R. Guerois, and S. Orlowski
Molecular Dynamics Simulations of E. coli MsbA Transmembrane Domain: Formation of a Semipore Structure
Biophys. J., October 1, 2006; 91(7): 2517 - 2531.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
E. K. Schmitt, M. Vrouenraets, and C. Steinem
Channel Activity of OmpF Monitored in Nano-BLMs
Biophys. J., September 15, 2006; 91(6): 2163 - 2171.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
S. Leekumjorn and A. K. Sum
Molecular Simulation Study of Structural and Dynamic Properties of Mixed DPPC/DPPE Bilayers
Biophys. J., June 1, 2006; 90(11): 3951 - 3965.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
M. Mahfoud, S. Sukumaran, P. Hulsmann, K. Grieger, and M. Niederweis
Topology of the Porin MspA in the Outer Membrane of Mycobacterium smegmatis
J. Biol. Chem., March 3, 2006; 281(9): 5908 - 5915.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
C. Danelon, E. M. Nestorovich, M. Winterhalter, M. Ceccarelli, and S. M. Bezrukov
Interaction of Zwitterionic Penicillins with the OmpF Channel Facilitates Their Translocation
Biophys. J., March 1, 2006; 90(5): 1617 - 1627.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
P. S. Niemela, M. T. Hyvonen, and I. Vattulainen
Influence of Chain Length and Unsaturation on Sphingomyelin Bilayers
Biophys. J., February 1, 2006; 90(3): 851 - 863.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
S. Varma, S.-W. Chiu, and E. Jakobsson
The Influence of Amino Acid Protonation States on Molecular Dynamics Simulations of the Bacterial Porin OmpF
Biophys. J., January 1, 2006; 90(1): 112 - 123.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
C. Peter and G. Hummer
Ion Transport through Membrane-Spanning Nanopores Studied by Molecular Dynamics Simulations and Continuum Electrostatics Calculations
Biophys. J., October 1, 2005; 89(4): 2222 - 2234.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
A. C. Saladino, Y. Xu, and P. Tang
Homology Modeling and Molecular Dynamics Simulations of Transmembrane Domain Structure of Human Neuronal Nicotinic Acetylcholine Receptor
Biophys. J., February 1, 2005; 88(2): 1009 - 1017.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
S. S. Deol, P. J. Bond, C. Domene, and M. S. P. Sansom
Lipid-Protein Interactions of Integral Membrane Proteins: A Comparative Simulation Study
Biophys. J., December 1, 2004; 87(6): 3737 - 3749.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
P. Niemela, M. T. Hyvonen, and I. Vattulainen
Structure and Dynamics of Sphingomyelin Bilayer: Insight Gained through Systematic Comparison to Phosphatidylcholine
Biophys. J., November 1, 2004; 87(5): 2976 - 2989.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
M. Baaden and M. S. P. Sansom
OmpT: Molecular Dynamics Simulations of an Outer Membrane Enzyme
Biophys. J., November 1, 2004; 87(5): 2942 - 2953.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
H. Miedema, A. Meter-Arkema, J. Wierenga, J. Tang, B. Eisenberg, W. Nonner, H. Hektor, D. Gillespie, and W. Meijberg
Permeation Properties of an Engineered Bacterial OmpF Porin Containing the EEEE-Locus of Ca2+ Channels
Biophys. J., November 1, 2004; 87(5): 3137 - 3147.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
A. Alcaraz, E. M. Nestorovich, M. Aguilella-Arzo, V. M. Aguilella, and S. M. Bezrukov
Salting Out the Ionic Selectivity of a Wide Channel: The Asymmetry of OmpF
Biophys. J., August 1, 2004; 87(2): 943 - 957.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
F. Y. Jiang, Y. Bouret, and J. T. Kindt
Molecular Dynamics Simulations of the Lipid Bilayer Edge
Biophys. J., July 1, 2004; 87(1): 182 - 192.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
K. Yu, W. Fu, H. Liu, X. Luo, K. X. Chen, J. Ding, J. Shen, and H. Jiang
Computational Simulations of Interactions of Scorpion Toxins with the Voltage-Gated Potassium Ion Channel
Biophys. J., June 1, 2004; 86(6): 3542 - 3555.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
M. O. Jensen, O. G. Mouritsen, and G. H. Peters
Simulations of a Membrane-Anchored Peptide: Structure, Dynamics, and Influence on Bilayer Properties
Biophys. J., June 1, 2004; 86(6): 3556 - 3575.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
E. Olkhova, M. C. Hutter, M. A. Lill, V. Helms, and H. Michel
Dynamic Water Networks in Cytochrome c Oxidase from Paracoccus denitrificans Investigated by Molecular Dynamics Simulations
Biophys. J., April 1, 2004; 86(4): 1873 - 1889.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
S. Varma and E. Jakobsson
Ionization States of Residues in OmpF and Mutants: Effects of Dielectric Constant and Interactions between Residues
Biophys. J., February 1, 2004; 86(2): 690 - 704.
[Abstract] [Full Text] [PDF]

Home page
 Microbiol. Mol. Biol. Rev.Home page
H. Nikaido
Molecular Basis of Bacterial Outer Membrane Permeability Revisited
Microbiol. Mol. Biol. Rev., December 1, 2003; 67(4): 593 - 656.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
E. M. Nestorovich, T. K. Rostovtseva, and S. M. Bezrukov
Residue Ionization and Ion Transport through OmpF Channels
Biophys. J., December 1, 2003; 85(6): 3718 - 3729.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
D. Lu, P. Grayson, and K. Schulten
Glycerol Conductance and Physical Asymmetry of the Escherichia coli Glycerol Facilitator GlpF
Biophys. J., November 1, 2003; 85(5): 2977 - 2987.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
J. D. Faraldo-Gomez, G. R. Smith, and M. S. P. Sansom
Molecular Dynamics Simulations of the Bacterial Outer Membrane Protein FhuA: A Comparative Study of the Ferrichrome-Free and Bound States
Biophys. J., September 1, 2003; 85(3): 1406 - 1420.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
D. E. Elmore and D. A. Dougherty
Investigating Lipid Composition Effects on the Mechanosensitive Channel of Large Conductance (MscL) Using Molecular Dynamics Simulations
Biophys. J., September 1, 2003; 85(3): 1512 - 1524.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
U. Zachariae, V. Helms, and H. Engelhardt
Multistep Mechanism of Chloride Translocation in a Strongly Anion-Selective Porin Channel
Biophys. J., August 1, 2003; 85(2): 954 - 962.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
T. Bastug and S. Kuyucak
Role of the Dielectric Constants of Membrane Proteins and Channel Water in Ion Permeation
Biophys. J., May 1, 2003; 84(5): 2871 - 2882.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
G. Colombo, S. J. Marrink, and A. E. Mark
Simulation of MscL Gating in a Bilayer under Stress
Biophys. J., April 1, 2003; 84(4): 2331 - 2337.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
S. Bransburg-Zabary, E. Nachliel, and M. Gutman
Gauging of the PhoE Channel by a Single Freely Diffusing Proton
Biophys. J., December 1, 2002; 83(6): 2987 - 3000.
[Abstract] [Full Text] [PDF]

Home page
 ScienceHome page
M. H. Bracey, M. A. Hanson, K. R. Masuda, R. C. Stevens, and B. F. Cravatt
Structural Adaptations in a Membrane Enzyme That Terminates Endocannabinoid Signaling
Science, November 29, 2002; 298(5599): 1793 - 1796.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
I. H. Shrivastava, D. P. Tieleman, P. C. Biggin, and M. S. P. Sansom
K+ versus Na+ Ions in a K Channel Selectivity Filter: A Simulation Study
Biophys. J., August 1, 2002; 83(2): 633 - 645.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
P. J. Bond, J. D. Faraldo-Gomez, and M. S. P. Sansom
OmpA: A Pore or Not a Pore? Simulation and Modeling Studies
Biophys. J., August 1, 2002; 83(2): 763 - 775.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
M. O. Jensen, S. Park, E. Tajkhorshid, and K. Schulten
Energetics of glycerol conduction through aquaglyceroporin GlpF
PNAS, May 14, 2002; 99(10): 6731 - 6736.
[Abstract] [Full Text] [PDF]

Home page
 ScienceHome page
B. L. de Groot and H. Grubmuller
Water Permeation Across Biological Membranes: Mechanism and Dynamics of Aquaporin-1 and GlpF
Science, December 14, 2001; 294(5550): 2353 - 2357.
[Abstract] [Full Text] [PDF]

Home page
 Antimicrob. Agents Chemother.Home page
V. Simonet, M. Malléa, and J.-M. Pagès
Substitutions in the Eyelet Region Disrupt Cefepime Diffusion through the Escherichia coli OmpF Channel
Antimicrob. Agents Chemother., February 1, 2000; 44(2): 311 - 315.
[Abstract] [Full Text]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Copyright © 1998 by the Biophysical Society.