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

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


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Circular Dichroism
  • Crystallography, X-Ray
  • Hydrogen Bonding
  • Models, Molecular*
  • Protein Conformation
  • Protein Engineering / methods*
  • Protein Folding*
  • Proteins / chemical synthesis
  • Proteins / chemistry*


  • Proteins