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: May 9, 2017, 10:34 p.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
4P61 2014-08-27 1.34 CHICKEN TRIOSEPHOSPHATE ISOMERASE WITH LOOP6 MUTATIONS, V167P AND W168E.
1SW0 2004-08-24 1.71 Triosephosphate isomerase from Gallus gallus, loop 6 hinge mutant K174L, T175W
1TPH 1994-04-30 1.8 1.8 ANGSTROMS CRYSTAL STRUCTURE OF WILD TYPE CHICKEN TRIOSEPHOSPHATE ISOMERASE-PHOSPHOGLYCOLOHYDROXAMATE COMPLEX
1TPB 1995-02-14 1.9 OFFSET OF A CATALYTIC LESION BY A BOUND WATER SOLUBLE
1TPW 1995-04-20 1.9 TRIOSEPHOSPHATE ISOMERASE DRINKS WATER TO KEEP HEALTHY
1TPV 1995-04-20 1.9 S96P CHANGE IS A SECOND-SITE SUPPRESSOR FOR H95N SLUGGISH MUTANT TRIOSEPHOSPHATE ISOMERASE
1TPC 1995-02-14 1.9 OFFSET OF A CATALYTIC LESION BY A BOUND WATER SOLUBLE
1TPU 1995-04-20 1.9 S96P CHANGE IS A SECOND-SITE SUPPRESSOR FOR H95N SLUGGISH MUTANT TRIOSEPHOSPHATE ISOMERASE
1SW3 2004-08-24 2.03 Triosephosphate isomerase from Gallus gallus, loop 6 mutant T175V
1SPQ 2004-08-24 2.16 Understanding protein lids: Structural analysis of active hinge mutants in triosephosphate isomerase
1SW7 2004-08-24 2.22 Triosephosphate isomerase from Gallus gallus, loop 6 mutant K174N, T175S, A176S
8TIM 1999-02-16 2.5 TRIOSE PHOSPHATE ISOMERASE
1TIM 1976-10-15 2.5 STRUCTURE OF TRIOSE PHOSPHATE ISOMERASE FROM CHICKEN MUSCLE
1SU5 2004-08-24 2.7 Understanding protein lids: Structural analysis of active hinge mutants in triosephosphate isomerase
1SQ7 2004-08-24 2.85 Understanding protein lids: Structural analysis of active hinge mutants in triosephosphate isomerase
1SSG 2004-08-24 2.9 Understanding protein lids: Structural analysis of active hinge mutants in triosephosphate isomerase
1SSD 2004-08-24 2.9 Understanding protein lids: Structural analysis of active hinge mutants in triosephosphate isomerase

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