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

Po-Ssu Huang, Kaspar Feldmeier, Fabio Parmeggiani, D Alejandro Fernandez Velasco, Birte Höcker, David Baker

Research output: Contribution to journalArticle (Academic Journal)

301 Downloads (Pure)

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.

Original languageEnglish
Pages (from-to)29-34
Number of pages6
JournalNature Chemical Biology
Volume12
Issue number1
Early online date23 Nov 2015
DOIs
Publication statusPublished - Jan 2016

Structured keywords

  • Bristol BioDesign Institute

Keywords

  • Circular Dichroism
  • Crystallography, X-Ray
  • Hydrogen Bonding
  • Models, Molecular
  • Protein Conformation
  • Protein Engineering
  • Protein Folding
  • Proteins
  • Chemical genetics
  • Target identification
  • Target validation
  • synthetic biology

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