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

Titelangaben

Huang, Po-Ssu ; Feldmeier, Kaspar ; Parmeggiani, Fabio ; Velasco, D Alejandro Fernandez ; Höcker, Birte ; Baker, David:
De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy.
In: Nature Chemical Biology. Bd. 12 (2016) Heft 1 . - S. 29-34.
ISSN 1552-4469
DOI: https://doi.org/10.1038/nchembio.1966

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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.