Perturbing the energy landscape for improved packing during computational protein design
Open accessAbstract
The FastDesign protocol in the molecular modeling program Rosetta iterates between sequence optimization and structure refinement to stabilize de novo designed protein structures and complexes. FastDesign has been used previously to design novel protein folds and assemblies with important applications in research and medicine. To promote sampling of alternative conformations and sequences, FastDesign includes stages where the energy landscape is smoothened by reducing repulsive forces. Here, we discover that this process disfavors larger amino acids in the protein core because the protein compresses in the early stages of refinement. By testing alternative ramping strategies for the repulsive weight, we arrive at a scheme that produces lower energy designs with more native‐like sequence composition in the protein core. We further validate the protocol by designing and experimentally characterizing over 4000 proteins and show that the new protocol produces higher stability proteins.
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Using fragment assembly, piecewise fragment assembly and helical extension, the authors designed a large set of miniproteins that ranged in length from 50 to 65 amino acids and contained larger hydrophobic cores than previous miniprotein scaffold libraries.
“Using fragment assembly7, piecewise fragment assembly8 and helical extension9, we designed a large set of miniproteins that ranged in length from 50 to 65 amino acids and contained larger hydrophobic cores than previous miniprotein scaffold libraries1.”
From Design of protein-binding proteins from the target structure alone (2022) · cites this paper as [9]
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“WeranRosetta 3.13, downloaded from the of fi cial website of RosettaCommons 42,43 .”
Influential
- Authors
- Maguire, J. B., Haddox, H. K., Strickland, D., Halabiya, S. F., Coventry, B., Griffin, J. R., Pulavarti, S. V. S. R. K., Cummins, M., Thieker, D. F., Klavins, E., Szyperski, T., DiMaio, F., Baker, D., & Kuhlman, B.
- Affiliations
- University of North Carolina at Chapel Hill (US)
- University of Washington (US)
- University at Buffalo, State University of New York (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Kuhlman, Brian
- ORCID
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 2020-12-11
- Volume
- 89
- Issue
- 4
- Pages
- 436-449
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- PMC
- PMC8299543
- OpenAlex
- W3109508638
- Cited by
- 169
- References
- 29
- Citations by year
- 2026: 32 · 2025: 39 · 2024: 30 · 2023: 25 · 2022: 34 · 2021: 8 · 2020: 1
- FWCI
- 5.52
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Proteins Structure Function and Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Carolina Digital Repository (University of North Carolina at Chapel Hill) (submittedVersion)
- Funders
- Defense Advanced Research Projects Agency (FA8750‐17‐C‐0219)
- The National Cancer Institute (T32CA009156)
- National Institute of General Medical Sciences (R01GM123089, R35GM131923)
- National Science Foundation (MBC1615570)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
- Keywords
- computational protein design, protein packing, protein stability, sequence optimization, structure refinement, Rosetta
- MeSH terms
- Protein Conformation, Proteins, Protein Engineering, Protein Folding, Computational Biology, Databases, Protein, Protein Stability, Hydrophobic and Hydrophilic Interactions
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