ArticlePLoS computational biology2019
A lipophilicity-based energy function for membrane-protein modelling and design.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed.
- Membrane Protein Insertion in Cells: Principles, Pathways, and Quality Control.Chemical reviews · 2026Review
- The sequence and structural integrity of the SARS-CoV-2 Spike protein transmembrane domain is crucial for viral entry.Communications biology · 2025Article
- Design principles of the common Gly-X6-Gly membrane protein building block.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- De novo-designed transmembrane proteins bind and regulate a cytokine receptor.Nature chemical biology · 2024Article
- One-shot design elevates functional expression levels of a voltage-gated potassium channel.Protein science : a publication of the Protein Society · 2024Article
- Modeling membrane geometries implicitly in Rosetta.Protein science : a publication of the Protein Society · 2024Article
- Computational design and molecular dynamics simulations suggest the mode of substrate binding in ceramide synthases.Nature communications · 2023Article
- UNILIPID, a Methodology for Energetically Accurate Prediction of Protein Insertion into Implicit Membranes of Arbitrary Shape.Membranes · 2023Article
- Computational design of BclxL inhibitors that target transmembrane domain interactions.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
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- In Silico Screening of Bioactive Compounds of Representative Seaweeds to Inhibit SARS-CoV-2 ACE2-Bound Omicron B.1.1.529 Spike Protein Trimer.Marine drugs · 2022Article
- Diverse Scientific Benchmarks for Implicit Membrane Energy Functions.Journal of chemical theory and computation · 2021Article
- Computational structure prediction provides a plausible mechanism for electron transfer by the outer membrane protein Cyc2 from Acidithiobacillus ferrooxidans.Protein science : a publication of the Protein Society · 2021Article
- Membrane proteins enter the fold.Current opinion in structural biology · 2021Review
- Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER distance restraints.PLoS computational biology · 2021Article
- Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design.Biochemistry · 2021Review
- Prediction of amphipathic helix-membrane interactions with Rosetta.PLoS computational biology · 2021Article
- Local Bilayer Hydrophobicity Modulates Membrane Protein Stability.Journal of the American Chemical Society · 2021Article
- Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane.Biophysical journal · 2020Article
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3 authors.
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Abstract
Membrane-protein design is an exciting and increasingly successful research area which has led to landmarks including the design of stable and accurate membrane-integral proteins based on coiled-coil motifs. Design of topologically more complex proteins, such as most receptors, channels, and transporters, however, demands an energy function that balances contributions from intra-protein contacts and protein-membrane interactions. Recent advances in water-soluble all-atom energy functions have increased the accuracy in structure-prediction benchmarks. The plasma membrane, however, imposes different physical constraints on protein solvation. To understand these constraints, we recently developed a high-throughput experimental screen, called dsTβL, and inferred apparent insertion energies for each amino acid at dozens of positions across the bacterial plasma membrane. Here, we express these profiles as lipophilicity energy terms in Rosetta and demonstrate that the new energy function outperforms previous ones in modelling and design benchmarks. Rosetta ab initio simulations starting from an extended chain recapitulate two-thirds of the experimentally determined structures of membrane-spanning homo-oligomers with <2.5Å root-mean-square deviation within the top-predicted five models (available online: http://tmhop.weizmann.ac.il). Furthermore, in two sequence-design benchmarks, the energy function improves discrimination of stabilizing point mutations and recapitulates natural membrane-protein sequences of known structure, thereby recommending this new energy function for membrane-protein modelling and design.
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