ArticleEuropean biophysics journal : EBJ2008
Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers.
Article in European biophysics journal : EBJ, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 23 citations in OpenAlex.
- BioSpring: An elastic network framework for interactive exploration of macromolecular mechanics.Protein science : a publication of the Protein Society · 2025Article
- What have molecular simulations contributed to understanding of Gram-negative bacterial cell envelopes?Microbiology (Reading, England) · 2022Review
- Prediction of the Closed Conformation and Insights into the Mechanism of the Membrane Enzyme LpxR.Biophysical journal · 2018Article
- Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies.Chemical reviews · 2018Review
- Full-Length OmpA: Structure, Function, and Membrane Interactions Predicted by Molecular Dynamics Simulations.Biophysical journal · 2016Article
- Properties and Phylogeny of 76 Families of Bacterial and Eukaryotic Organellar Outer Membrane Pore-Forming Proteins.PloS one · 2016Article
- Molecular Simulations of Gram-Negative Bacterial Membranes: A Vignette of Some Recent Successes.Biophysical journal · 2015Review
- Resolving the native conformation of Escherichia coli OmpA.The FEBS journal · 2010Article
- Article
- Solution NMR mapping of water-accessible residues in the transmembrane beta-barrel of OmpX.European biophysics journal : EBJ · 2010Article
- Gating at both ends and breathing in the middle: conformational dynamics of TolC.Biophysical journal · 2008Article
- Molecular dynamics simulations and membrane protein structure quality.European biophysics journal : EBJ · 2008Article
- Coarse-grained models reveal functional dynamics--I. Elastic network models--theories, comparisons and perspectives.Bioinformatics and biology insights · 2008Article
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
The structures of three bacterial outer membrane proteins (OmpA, OmpX and PagP) have been determined by both X-ray diffraction and NMR. We have used multiple (7 x 15 ns) MD simulations to compare the conformational dynamics resulting from the X-ray versus the NMR structures, each protein being simulated in a lipid (DMPC) bilayer. Conformational drift was assessed via calculation of the root mean square deviation as a function of time. On this basis the 'quality' of the starting structure seems mainly to influence the simulation stability of the transmembrane beta-barrel domain. Root mean square fluctuations were used to compare simulation mobility as a function of residue number. The resultant residue mobility profiles were qualitatively similar for the corresponding X-ray and NMR structure-based simulations. However, all three proteins were generally more mobile in the NMR-based than in the X-ray simulations. Principal components analysis was used to identify the dominant motions within each simulation. The first two eigenvectors (which account for >50% of the protein motion) reveal that such motions are concentrated in the extracellular loops and, in the case of PagP, in the N-terminal alpha-helix. Residue profiles of the magnitude of motions corresponding to the first two eigenvectors are similar for the corresponding X-ray and NMR simulations, but the directions of these motions correlate poorly reflecting incomplete sampling on a approximately 10 ns timescale.
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