ArticleBiophysical journal2018
A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations.
Article in Biophysical journal, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
7 citing papers in PubMed.
- Membrane Protein Folding and Biogenesis: Insights from Single-Molecule Force Spectroscopy.Chemical reviews · 2026Review
- Steric trapping strategy for studying the folding of helical membrane proteins.Methods (San Diego, Calif.) · 2024Review
- Lipid bilayer induces contraction of the denatured state ensemble of a helical-bundle membrane protein.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- On the Interpretation of Force-Induced Unfolding Studies of Membrane Proteins Using Fast Simulations.Biophysical journal · 2019Article
- Computational Modeling of Realistic Cell Membranes.Chemical reviews · 2019Review
- Site-Specific Peptide Probes Detect Buried Water in a Lipid Membrane.Biophysical journal · 2019Article
- A Multi-Scale Approach to Membrane Remodeling Processes.Frontiers in molecular biosciences · 2019Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
We use the statistics of a large and curated training set of transmembrane helical proteins to develop a knowledge-based potential that accounts for the dependence on both the depth of burial of the protein in the membrane and the degree of side-chain exposure. Additionally, the statistical potential includes depth-dependent energies for unsatisfied backbone hydrogen bond donors and acceptors, which are found to be relatively small, ∼2 RT. Our potential accurately places known proteins within the bilayer. The potential is applied to the mechanosensing MscL channel in membranes of varying thickness and curvature, as well as to the prediction of protein structure. The potential is incorporated into our new Upside molecular dynamics algorithm. Notably, we account for the exchange of protein-lipid interactions for protein-protein interactions as helices contact each other, thereby avoiding overestimating the energetics of helix association within the membrane. Simulations of most multimeric complexes find that isolated monomers and the oligomers retain the same orientation in the membrane, suggesting that the assembly of prepositioned monomers presents a viable mechanism of oligomerization.
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Registered trials
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