ArticleProceedings of the National Academy of Sciences of the United States of America2006
Membrane protein dynamics and detergent interactions within a crystal: a simulation study of OmpA.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- BioSpring: An elastic network framework for interactive exploration of macromolecular mechanics.Protein science : a publication of the Protein Society · 2025Article
- The structural integrity of the membrane-embedded bacterial division complex FtsQBL studied with molecular dynamics simulations.Computational and structural biotechnology journal · 2023Article
- New Malonate-Derived Tetraglucoside Detergents for Membrane Protein Stability.ACS chemical biology · 2020Article
- Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics.International journal of molecular sciences · 2018Review
- Prediction of the Closed Conformation and Insights into the Mechanism of the Membrane Enzyme LpxR.Biophysical journal · 2018Article
- Temperature dependence of protein-water interactions in a gated yeast aquaporin.Scientific reports · 2017Article
- Dimerization of the EphA1 receptor tyrosine kinase transmembrane domain: Insights into the mechanism of receptor activation.Biochemistry · 2014Article
- Article
- Dodecyl maltoside protects membrane proteins in vacuo.Biophysical journal · 2013Article
- Detergent-mediated protein aggregation.Chemistry and physics of lipids · 2013Review
- Membrane protein dynamics in different environments: simulation study of the outer membrane protein X in a lipid bilayer and in a micelle.European biophysics journal : EBJ · 2011Article
- Microscopic rotary mechanism of ion translocation in the F(o) complex of ATP synthases.Nature chemical biology · 2010Article
- Article
- Conformational exchange in a membrane transport protein is altered in protein crystals.Biophysical journal · 2010Article
- Solution and crystal molecular dynamics simulation study of m4-cyanovirin-N mutants complexed with di-mannose.Biophysical journal · 2009Article
- Model structure of APOBEC3C reveals a binding pocket modulating ribonucleic acid interaction required for encapsidation.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Insights into protein-polysorbate interactions analysed by means of isothermal titration and differential scanning calorimetry.European biophysics journal : EBJ · 2009Article
- Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers.European biophysics journal : EBJ · 2008Article
- Structure refinement of the OpcA adhesin using molecular dynamics.Biophysical journal · 2007Article
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4 authors.
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Abstract
Molecular dynamics (MD) simulations are used to explore the dynamics of a membrane protein in its crystal environment. A 50-ns-duration simulation (at a temperature of 300 K) is performed for the crystallographic unit cell of the bacterial outer membrane protein OmpA. The unit cell contains four protein molecules, plus detergent molecules and water. An excellent correlation between simulated and experimental values of crystallographic B factors is observed. Effectively, 0.2 micros of protein trajectories are obtained, allowing a critical assessment of simulation quality. Some deficiency in conformational sampling is demonstrated, but averaging over multiple trajectories improves this limitation. The previously undescribed structure and dynamics of detergent molecules in a unit cell are reported here, providing insight into the interactions important in the formation and stabilization of the crystalline environment at room temperature. In particular, we show that at room temperature the detergent molecules form a dynamic, extended micellar structure spreading over adjacent OmpA monomers within the crystal.
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