title: De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy.
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.
authors.affiliation: Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.|Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA.
authors.forename: Po-Ssu
authors.initials: PS
authors.lastname: Huang
authors.affiliation: Max Planck Institute for Developmental Biology, Tübingen, Germany.
authors.forename: Kaspar
authors.initials: K
authors.lastname: Feldmeier
authors.affiliation: Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.|Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA.
authors.forename: Fabio
authors.initials: F
authors.lastname: Parmeggiani
authors.affiliation: Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, México D.F., 04510 Mexico.
authors.forename: D Alejandro Fernandez
authors.initials: DAF
authors.lastname: Velasco
authors.affiliation: Max Planck Institute for Developmental Biology, Tübingen, Germany.
authors.forename: Birte
authors.initials: B
authors.lastname: Höcker
authors.affiliation: Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.|Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA.|Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.
authors.forename: David
authors.initials: D
authors.lastname: Baker
mesh_terms: D002942:Circular Dichroism; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D008958:Models, Molecular; D011487:Protein Conformation; D015202:Protein Engineering / Q000379:methods*; D017510:Protein Folding; D011506:Proteins / Q000138:chemical synthesis / Q000737:chemistry*
chemical_list: D011506:Proteins