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.

Submission Details

ID: 42WeVJh83

Submitter: Connie Wang

Submission Date: July 31, 2017, 11:46 a.m.

Version: 1

Publication Details
Huang PS;Feldmeier K;Parmeggiani F;Velasco DAF;Höcker B;Baker D,Nat Chem Biol (2016) De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy. PMID:26595462
Additional Information

Study Summary

Number of data points 29
Proteins Triosephosphate isomerase
Unique complexes 29
Assays/Quantities/Protocols Experimental Assay: Tm
Libraries De novo design of symmetric TIM-barrel proteins

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
1SPQ 2004-03-17T00:00:00+0000 2.16 Understanding protein lids: Structural analysis of active hinge mutants in triosephosphate isomerase
1SQ7 2004-03-18T00:00:00+0000 2.85 Understanding protein lids: Structural analysis of active hinge mutants in triosephosphate isomerase
1SSD 2004-03-24T00:00:00+0000 2.9 Understanding protein lids: Structural analysis of active hinge mutants in triosephosphate isomerase
1SSG 2004-03-24T00:00:00+0000 2.9 Understanding protein lids: Structural analysis of active hinge mutants in triosephosphate isomerase
1SU5 2004-03-26T00:00:00+0000 2.7 Understanding protein lids: Structural analysis of active hinge mutants in triosephosphate isomerase
1SW0 2004-03-30T00:00:00+0000 1.71 Triosephosphate isomerase from Gallus gallus, loop 6 hinge mutant K174L, T175W
1SW3 2004-03-30T00:00:00+0000 2.03 Triosephosphate isomerase from Gallus gallus, loop 6 mutant T175V
1SW7 2004-03-30T00:00:00+0000 2.22 Triosephosphate isomerase from Gallus gallus, loop 6 mutant K174N, T175S, A176S
1TIM 1976-09-01T00:00:00+0000 2.5 STRUCTURE OF TRIOSE PHOSPHATE ISOMERASE FROM CHICKEN MUSCLE
1TPB 1994-02-03T00:00:00+0000 1.9 OFFSET OF A CATALYTIC LESION BY A BOUND WATER SOLUBLE

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
90.3 Triosephosphate isomerase P54714 TPIS_CANLF
100.0 Triosephosphate isomerase P00940 TPIS_CHICK