ArticleBiophysical journal2008
Structural refinement of membrane proteins by restrained molecular dynamics and solvent accessibility data.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 26 citations in OpenAlex.
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- A novel approach to modeling side chain ensembles of the bifunctional spin label RX.bioRxiv : the preprint server for biology · 2023Article
- Hybrid Refinement of Heterogeneous Conformational Ensembles Using Spectroscopic Data.The journal of physical chemistry letters · 2019Article
- Resting state of the human proton channel dimer in a lipid bilayer.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.PLoS computational biology · 2015Article
- Distance measurement between two flexible sites in proteins in high viscosity medium at physiological temperature using continuous wave EPR.Protein & cell · 2014Article
- Molecular mechanism of Mg2+-dependent gating in CorA.Nature communications · 2014Article
- Structural basis of lipid-driven conformational transitions in the KvAP voltage-sensing domain.Nature structural & molecular biology · 2014Article
- Influences of membrane mimetic environments on membrane protein structures.Annual review of biophysics · 2013Review
- Modeling and simulation of ion channels.Chemical reviews · 2012Review
- Structural investigation of MscL gating using experimental data and coarse grained MD simulations.PLoS computational biology · 2012Article
- Toward the fourth dimension of membrane protein structure: insight into dynamics from spin-labeling EPR spectroscopy.Structure (London, England : 1993) · 2011Review
- Structural dynamics of the magnesium-bound conformation of CorA in a lipid bilayer.Structure (London, England : 1993) · 2010Article
- The activated state of a sodium channel voltage sensor in a membrane environment.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Structural studies of the Enterococcus faecalis SufU [Fe-S] cluster protein.BMC biochemistry · 2009Article
- A structural mechanism for MscS gating in lipid bilayers.Science (New York, N.Y.) · 2008Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
We present an approach for incorporating solvent accessibility data from electron paramagnetic resonance experiments in the structural refinement of membrane proteins through restrained molecular dynamics simulations. The restraints have been parameterized from oxygen (PiO(2)) and nickel-ethylenediaminediacetic acid (PiNiEdda) collision frequencies, as indicators of lipid or aqueous exposed spin-label sites. These are enforced through interactions between a pseudoatom representation of the covalently attached Nitroxide spin-label and virtual "solvent" particles corresponding to O(2) and NiEdda in the surrounding environment. Interactions were computed using an empirical potential function, where the parameters have been optimized to account for the different accessibilities of the spin-label pseudoatoms to the surrounding environment. This approach, "pseudoatom-driven solvent accessibility refinement", was validated by refolding distorted conformations of the Streptomyces lividans potassium channel (KcsA), corresponding to a range of 2-30 A root mean-square deviations away from the native structure. Molecular dynamics simulations based on up to 58 electron paramagnetic resonance restraints derived from spin-label mutants were able to converge toward the native structure within 1-3 A root mean-square deviations with minimal computational cost. The use of energy-based ranking and structure similarity clustering as selection criteria helped in the convergence and identification of correctly folded structures from a large number of simulations. This approach can be applied to a variety of integral membrane protein systems, regardless of oligomeric state, and should be particularly useful in calculating conformational changes from a known reference crystal structure.
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