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Nat Chem Biol. 2016 Jan;12(1):29-34. doi: 10.1038/nchembio.1966. Epub 2015 Nov 23.

De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy.

Author information

1
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.
2
Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA.
3
Max Planck Institute for Developmental Biology, Tübingen, Germany.
4
Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, México D.F., 04510 Mexico.
5
Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.
#
Contributed equally

Abstract

Despite efforts for over 25 years, de novo protein design has not succeeded in achieving the TIM-barrel fold. Here we describe the computational design of four-fold symmetrical (β/α)8 barrels guided by geometrical and chemical principles. Experimental characterization of 33 designs revealed the importance of side chain-backbone hydrogen bonds for defining the strand register between repeat units. The X-ray crystal structure of a designed thermostable 184-residue protein is nearly identical to that of the designed TIM-barrel model. PSI-BLAST searches do not identify sequence similarities to known TIM-barrel proteins, and sensitive profile-profile searches indicate that the design sequence is distant from other naturally occurring TIM-barrel superfamilies, suggesting that Nature has sampled only a subset of the sequence space available to the TIM-barrel fold. The ability to design TIM barrels de novo opens new possibilities for custom-made enzymes.

PMID:
26595462
PMCID:
PMC4684731
DOI:
10.1038/nchembio.1966
[Indexed for MEDLINE]
Free PMC Article

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