De novo design of knotted tandem repeat proteins

Lindsey A. Doyle, Brittany Takushi, Ryan D. Kibler, Lukas F. Milles, Carolina T. Orozco, Jonathan D. Jones, Sophie E. Jackson, Barry L. Stoddard () and Philip Bradley ()
Additional contact information
Lindsey A. Doyle: Fred Hutchinson Cancer Center
Brittany Takushi: Fred Hutchinson Cancer Center
Ryan D. Kibler: University of Washington
Lukas F. Milles: University of Washington
Carolina T. Orozco: University of Cambridge, Lensfield Road
Jonathan D. Jones: University of Cambridge, Lensfield Road
Sophie E. Jackson: University of Cambridge, Lensfield Road
Barry L. Stoddard: Fred Hutchinson Cancer Center
Philip Bradley: Fred Hutchinson Cancer Center

Nature Communications, 2023, vol. 14, issue 1, 1-17

Abstract: Abstract De novo protein design methods can create proteins with folds not yet seen in nature. These methods largely focus on optimizing the compatibility between the designed sequence and the intended conformation, without explicit consideration of protein folding pathways. Deeply knotted proteins, whose topologies may introduce substantial barriers to folding, thus represent an interesting test case for protein design. Here we report our attempts to design proteins with trefoil (31) and pentafoil (51) knotted topologies. We extended previously described algorithms for tandem repeat protein design in order to construct deeply knotted backbones and matching designed repeat sequences (N = 3 repeats for the trefoil and N = 5 for the pentafoil). We confirmed the intended conformation for the trefoil design by X ray crystallography, and we report here on this protein’s structure, stability, and folding behaviour. The pentafoil design misfolded into an asymmetric structure (despite a 5-fold symmetric sequence); two of the four repeat-repeat units matched the designed backbone while the other two diverged to form local contacts, leading to a trefoil rather than pentafoil knotted topology. Our results also provide insights into the folding of knotted proteins.

Date: 2023
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-023-42388-y Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-42388-y

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-023-42388-y

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().