ArticleBiophysical journal2015
A Practical Implicit Membrane Potential for NMR Structure Calculations of Membrane Proteins.
Article in Biophysical journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Solution NMR Spectroscopy for the Determination of Structures of Membrane Proteins in a Lipid Environment.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Xplor-NIH: Better parameters and protocols for NMR protein structure determination.Protein science : a publication of the Protein Society · 2024Article
- A Cholesterol Dimer Stabilizes the Inactivated State of an Inward-Rectifier Potassium Channel.Angewandte Chemie (International ed. in English) · 2022Article
- Mechanism of negative membrane curvature generation by I-BAR domains.Structure (London, England : 1993) · 2021Article
- Solid-State NMR of Membrane Proteins in Lipid Bilayers: To Spin or Not To Spin?Accounts of chemical research · 2021Review
- Water Accessibility Refinement of the Extended Structure of KirBac1.1 in the Closed State.Frontiers in molecular biosciences · 2021Article
- Membrane proteins in magnetically aligned phospholipid polymer discs for solid-state NMR spectroscopy.Biochimica et biophysica acta. Biomembranes · 2020Article
- The host-defense peptide piscidin P1 reorganizes lipid domains in membranes and decreases activation energies in mechanosensitive ion channels.The Journal of biological chemistry · 2019Article
- A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations.Biophysical journal · 2018Article
- Solution structure and elevator mechanism of the membrane electron transporter CcdA.Nature structural & molecular biology · 2018Article
- Xplor-NIH for molecular structure determination from NMR and other data sources.Protein science : a publication of the Protein Society · 2018Article
- Structure of monomeric Interleukin-8 and its interactions with the N-terminal Binding Site-I of CXCR1 by solution NMR spectroscopy.Journal of biomolecular NMR · 2017Article
- Structure of the Ebola virus envelope protein MPER/TM domain and its interaction with the fusion loop explains their fusion activity.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Structural Insights into the Yersinia pestis Outer Membrane Protein Ail in Lipid Bilayers.The journal of physical chemistry. B · 2017Article
- Applications of NMR to membrane proteins.Archives of biochemistry and biophysics · 2017Review
- High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH.Journal of biomolecular NMR · 2017Article
- Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation.Journal of biomolecular NMR · 2015Article
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4 authors.
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Abstract
The highly anisotropic environment of the lipid bilayer membrane imposes significant constraints on the structures and functions of membrane proteins. However, NMR structure calculations typically use a simple repulsive potential that neglects the effects of solvation and electrostatics, because explicit atomic representation of the solvent and lipid molecules is computationally expensive and impractical for routine NMR-restrained calculations that start from completely extended polypeptide templates. Here, we describe the extension of a previously described implicit solvation potential, eefxPot, to include a membrane model for NMR-restrained calculations of membrane protein structures in XPLOR-NIH. The key components of eefxPot are an energy term for solvation free energy that works together with other nonbonded energy functions, a dedicated force field for conformational and nonbonded protein interaction parameters, and a membrane function that modulates the solvation free energy and dielectric screening as a function of the atomic distance from the membrane center, relative to the membrane thickness. Initial results obtained for membrane proteins with structures determined experimentally in lipid bilayer membranes show that eefxPot affords significant improvements in structural quality, accuracy, and precision. Calculations with eefxPot are straightforward to implement and can be used to both fold and refine structures, as well as to run unrestrained molecular-dynamics simulations. The potential is entirely compatible with the full range of experimental restraints measured by various techniques. Overall, it provides a useful and practical way to calculate membrane protein structures in a physically realistic environment.
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