Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers

No abstract is available for this paper.

• Publication year

  2008

• Venue

  European Biophysics Journal

• Publication date

  2008-02-01

• Fields of study

  Biology, Medicine, Materials Science, Chemistry

• Identifiers
  DOI 10.1007/s00249-007-0185-8PMID 17551722
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Membrane protein dynamics and detergent interactions within a crystal: a simulation study of OmpA.

  2006cited by this paper
• NMR structure determination of a membrane protein with two transmembrane helices in micelles: MerF of the bacterial mercury detoxification system.

  2005cited by this paper
• Spontaneous formation of detergent micelles around the outer membrane protein OmpX.

  2005cited by this paper
• Assessing precision and accuracy of protein structures derived from NMR data

  2005cited by this paper
• NMR Structure of Mistic, a Membrane-Integrating Protein for Membrane Protein Expression

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• Membrane protein structure quality in molecular dynamics simulation.

  2005cited by this paper
• Enterobacter aerogenes OmpX, a cation‐selective channel mar‐ and osmo‐regulated

  2004cited by this paper
• NMR structure of the integral membrane protein OmpX.

  2004influential reference
• A hydrocarbon ruler measures palmitate in the enzymatic acylation of endotoxin

  2004influential reference
• OmpT: molecular dynamics simulations of an outer membrane enzyme.

  2004influential reference
• Conformational sampling and dynamics of membrane proteins from 10‐nanosecond computer simulations

  2004cited by this paper
• The integral membrane enzyme PagP alternates between two dynamically distinct states.

  2004influential reference
• MD simulations of spontaneous membrane protein/detergent micelle formation.

  2004cited by this paper
• Relative stability of protein structures determined by X‐ray crystallography or NMR spectroscopy: A molecular dynamics simulation study

  2003influential reference
• Molecular dynamics simulations of the bacterial outer membrane protein FhuA: a comparative study of the ferrichrome-free and bound states.

  2003cited by this paper
• Molecular basis for microbial adhesion to geochemical surfaces: computer simulation of Pseudomonas aeruginosa adhesion to goethite.

  2003cited by this paper
• Engineering teams up with computer-simulation and visualization tools to probe biomolecular mechanisms.

  2003cited by this paper
• Membrane protein dynamics versus environment: simulations of OmpA in a micelle and in a bilayer.

  2003influential reference
• A molecular dynamics investigation of mono and dimeric states of the outer membrane enzyme OMPLA.

  2003cited by this paper
• Membrane protein simulations: ion channels and bacterial outer membrane proteins.

  2003cited by this paper
• NMR solution structure determination of membrane proteins reconstituted in detergent micelles

  2003cited by this paper
• Solution structure and dynamics of the outer membrane enzyme PagP by NMR

  2002influential reference
• Molecular structure of the outer bacterial membrane of Pseudomonas aeruginosa via classical simulation.

  2002cited by this paper
• Setting up and optimization of membrane protein simulations

  2002cited by this paper
• OmpA: a pore or not a pore? Simulation and modeling studies.

  2002influential reference
• Improving the quality of protein structures derived by NMR spectroscopy**

  2002cited by this paper
• GROMACS 3.0: a package for molecular simulation and trajectory analysis

  2001cited by this paper
• Structure of outer membrane protein A transmembrane domain by NMR spectroscopy

  2001influential reference
• Biophysical approaches to membrane protein structure determination.

  2001influential reference
• Computer simulation of the rough lipopolysaccharide membrane of Pseudomonas aeruginosa.

  2001cited by this paper
• Solution NMR studies of the integral membrane proteins OmpX and OmpA from Escherichia coli

  2001influential reference
• Modeling of loops in protein structures

  2000cited by this paper
• High-resolution structure of the OmpA membrane domain.

  2000cited by this paper
• β-Barrel membrane proteins

  2000cited by this paper
• beta-Barrel membrane proteins.

  2000cited by this paper
• Structure and function of bacterial outer membrane proteins: barrels in a nutshell

  2000cited by this paper
• The structure of the outer membrane protein OmpX from Escherichia coli reveals possible mechanisms of virulence.

  1999influential reference
• Beta-barrel proteins from bacterial outer membranes: structure, function and refolding.

  1999cited by this paper
• A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer.

  1998cited by this paper
• Structure of the outer membrane protein A transmembrane domain

  1998influential reference
• LINCS: A linear constraint solver for molecular simulations

  1997cited by this paper
• A Transmembrane Helix Dimer: Structure and Implications

  1997cited by this paper
• Comparative protein modeling by satisfaction of spatial restraints.

  1996cited by this paper
• The GROMOS96 Manual and User Guide

  1996cited by this paper
• VMD: visual molecular dynamics.

  1996cited by this paper
• HOLE: a program for the analysis of the pore dimensions of ion channel structural models.

  1996cited by this paper
• Comparative protein modeling by satisfaction of spatial restraints

  1995cited by this paper
• RASMOL: biomolecular graphics for all.

  1995cited by this paper
• PROCHECK: a program to check the stereochemical quality of protein structures

  1993cited by this paper
• Essential dynamics of proteins

  1993influential reference
• Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

  1993cited by this paper
• The pore dimensions of gramicidin A.

  1993cited by this paper
• Comparative protein modelling by satisfaction of spatial restraints.

  1993cited by this paper
• Large-amplitude nonlinear motions in proteins.

  1992influential reference
• WHAT IF: a molecular modeling and drug design program.

  1990cited by this paper
• Hydrophilicity of polar amino acid side-chains is markedly reduced by flanking peptide bonds.

  1988cited by this paper
• Molecular dynamics with coupling to an external bath

  1984influential reference
• Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features

  1983cited by this paper

• BioSpring: An elastic network framework for interactive exploration of macromolecular mechanics

  2025cites this paper
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  2023cites this paper
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  2022cites this paper
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  2022cites this paper
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  2018cites this paper
• Prediction of the Closed Conformation and Insights into the Mechanism of the Membrane Enzyme LpxR

  2018influential citation
• Cardiotoxins: Functional Role of Local Conformational Changes

  2017cites this paper
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  2016cites this paper
• Full-Length OmpA: Structure, Function, and Membrane Interactions Predicted by Molecular Dynamics Simulations

  2016cites this paper
• Molecular Simulations of Gram-Negative Bacterial Membranes: A Vignette of Some Recent Successes.

  2015influential citation
• Foundations of Biomolecular Simulations: A Critical Introduction to Homology Modeling, Molecular Dynamics Simulations, and Free Energy Calculations of Membrane Proteins

  2014cites this paper
• Dynamics of Klebsiella pneumoniae OmpA transmembrane domain: the four extracellular loops display restricted motion behavior in micelles and in lipid bilayers.

  2012cites this paper
• The effect of calcium on the conformation of cobalamin transporter BtuB

  2010cites this paper
• Le pubblicazioni scientifiche prodotte con il contributo del CASPUR nel Triennio 2007-2009

  2010cites this paper
• Resolving the native conformation of Escherichia coli OmpA

  2010cites this paper
• Solution NMR mapping of water-accessible residues in the transmembrane β-barrel of OmpX

  2010cites this paper
• One membrane protein, two structures and six environments: a comparative molecular dynamics simulation study of the bacterial outer membrane protein PagP

  2009cites this paper
• Coarse-Grained Models Reveal Functional Dynamics - I. Elastic Network Models – Theories, Comparisons and Perspectives

  2008cites this paper
• Molecular dynamics simulations and membrane protein structure quality

  2008influential citation
• Gating at both ends and breathing in the middle: conformational dynamics of TolC.

  2008cites this paper