7SQ5

Designed trefoil knot protein, variant 3

Summary for 7SQ5

• Entry DOI: 10.2210/pdb7sq5/pdb
• Descriptor: Designed trefoil knot protein, variant 3, SODIUM ION (3 entities in total)
• Functional Keywords: tandem repeat protein, trp, knot, trefoil, de novo protein
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 18529.29

Authors

Takushi, B.,Doyle, L.,Stoddard, B.L.,Bradley, P. (deposition date: 2021-11-04, release date: 2022-11-09, Last modification date: 2024-04-03)

Primary citation

Doyle, L.A.,Takushi, B.,Kibler, R.D.,Milles, L.F.,Orozco, C.T.,Jones, J.D.,Jackson, S.E.,Stoddard, B.L.,Bradley, P.
De novo design of knotted tandem repeat proteins.
Nat Commun, 14:6746-6746, 2023

PubMed 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 (3) and pentafoil (5) 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.

PubMed: 37875492
DOI: 10.1038/s41467-023-42388-y

Experimental method

X-RAY DIFFRACTION (2.205 Å)