ArticleBiophysical journal2002
OmpA: a pore or not a pore? Simulation and modeling studies.
Article in Biophysical journal, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Negative design enables cell-free expression and folding of designed transmembrane β-barrels.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Start Me Up: How Can Surrounding Gangliosides Affect Sodium-Potassium ATPase Activity and Steer towards Pathological Ion Imbalance in Neurons?Biomedicines · 2022Review
- What have molecular simulations contributed to understanding of Gram-negative bacterial cell envelopes?Microbiology (Reading, England) · 2022Review
- Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model.Journal of chemical information and modeling · 2017Article
- Braun's Lipoprotein Facilitates OmpA Interaction with the Escherichia coli Cell Wall.Biophysical journal · 2017Article
- Full-Length OmpA: Structure, Function, and Membrane Interactions Predicted by Molecular Dynamics Simulations.Biophysical journal · 2016Article
- Atomistic molecular-dynamics simulations enable prediction of the arginine permeation pathway through OccD1/OprD from Pseudomonas aeruginosa.Biophysical journal · 2014Article
- Mass spectrometry defines the C-terminal dimerization domain and enables modeling of the structure of full-length OmpA.Structure (London, England : 1993) · 2014Article
- The role of short-chain conjugated poly-(R)-3-hydroxybutyrate (cPHB) in protein folding.International journal of molecular sciences · 2013Review
- Modeling and simulation of ion channels.Chemical reviews · 2012Review
- Hydrophobic mismatch and lipid sorting near OmpA in mixed bilayers: atomistic and coarse-grained simulations.Biophysical journal · 2012Article
- Resolving the native conformation of Escherichia coli OmpA.The FEBS journal · 2010Article
- Fast-time scale dynamics of outer membrane protein A by extended model-free analysis of NMR relaxation data.Biochimica et biophysica acta · 2010Article
- OmpA of uropathogenic Escherichia coli promotes postinvasion pathogenesis of cystitis.Infection and immunity · 2009Article
- Outer membrane protein G: Engineering a quiet pore for biosensing.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers.European biophysics journal : EBJ · 2008Article
- Membrane simulations of OpcA: gating in the loops?Biophysical journal · 2007Article
- Molecular dynamics simulations of E. coli MsbA transmembrane domain: formation of a semipore structure.Biophysical journal · 2006Article
- Membrane protein dynamics and detergent interactions within a crystal: a simulation study of OmpA.Proceedings of the National Academy of Sciences of the United States of America · 2006Article
- Pseudomonas aeruginosa porin OprF: properties of the channel.The Journal of biological chemistry · 2006Article
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3 authors.
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Abstract
The bacterial outer membrane protein OmpA is composed of an N-terminal 171-residue beta-barrel domain (OmpA(171)) that spans the bilayer and a periplasmic, C-terminal domain of unknown structure. OmpA has been suggested to primarily serve a structural role, as no continuous pore through the center of the barrel can be discerned in the crystal structure of OmpA(171). However, several groups have recorded ionic conductances for bilayer-reconstituted OmpA(171). To resolve this apparent paradox we have used molecular dynamics (MD) simulations on OmpA(171) to explore the conformational dynamics of the protein, in particular the possibility of transient formation of a central pore. A total of 19 ns of MD simulations of OmpA(171) have been run, and the results were analyzed in terms of 1) comparative behavior of OmpA(171) in different bilayer and bilayer-mimetic environments, 2) solvation states of OmpA(171), and 3) pore characteristics in different MD simulations. Significant mobility was observed for residues and water molecules within the beta-barrel. A simulation in which putative gate region side chains of the barrel interior were held in a non-native conformation led to an open pore, with a predicted conductance similar to experimental measurements. The OmpA(171) pore has been shown to be somewhat more dynamic than suggested by the crystal structure. A gating mechanism is proposed to explain its documented channel properties, involving a flickering isomerization of Arg138, forming alternate salt bridges with Glu52 (closed state) and Glu128 (open state).
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