ArticleProtein science : a publication of the Protein Society2018
Computational design of membrane proteins using RosettaMembrane.
Article in Protein science : a publication of the Protein Society, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Protein Design Meets Single-Molecule Detection: Towards Programmable Nanopore Sensors.International journal of molecular sciences · 2025Review
- Validation of de novo designed water-soluble and transmembrane β-barrels by in silico folding and melting.Protein science : a publication of the Protein Society · 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
- Protein Design: From the Aspect of Water Solubility and Stability.Chemical reviews · 2022Review
- Molecular basis for the evolved instability of a human G-protein coupled receptor.Cell reports · 2021Article
- 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 Protein Engineering with Rosetta.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane.Biophysical journal · 2020Article
- Review
- A lipophilicity-based energy function for membrane-protein modelling and design.PLoS computational biology · 2019Article
- Article
- Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins.Proteins · 2018Article
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2 authors.
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Abstract
Computational membrane protein design is challenging due to the small number of high-resolution structures available to elucidate the physical basis of membrane protein structure, multiple functionally important conformational states, and a limited number of high-throughput biophysical assays to monitor function. However, structural determination of membrane proteins has made tremendous progress in the past years. Concurrently the field of soluble computational design has made impressive inroads. These developments allow us to tackle the formidable challenge of designing functional membrane proteins. Herein, Rosetta is benchmarked for membrane protein design. We evaluate strategies to cope with the often reduced quality of experimental membrane protein structures. Further, we test the usage of symmetry in design protocols, which is particularly important as many membrane proteins exist as homo-oligomers. We compare a soluble scoring function with a scoring function optimized for membrane proteins, RosettaMembrane. Both scoring functions recovered around half of the native sequence when completely redesigning membrane proteins. However, RosettaMembrane recovered the most native-like amino acid property composition. While leucine was overrepresented in the inner and outer-hydrophobic regions of RosettaMembrane designs, it resulted in a native-like surface hydrophobicity indicating that it is currently the best option for designing membrane proteins with Rosetta.
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