Stabilisation of a (βα) 8 -Barrel Protein Designed from Identical Half Barrels Tobias Seitz, Marco Bocola, Jörg Claren and Reinhard Sterner* Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany It has been suggested that the common (βα) 8 -barrel enzyme fold has evolved by the duplication and fusion of identical (βα) 4 -half barrels, followed by the optimisation of their interface. In our attempts to recons- truct these events in vitro we have previously linked in tandem two copies of the C-terminal half barrel HisF-C of imidazole glycerol phosphate synthase from Thermotoga maritima and subsequently reconstituted in the fusion construct HisF-CC a salt bridge cluster present in wild-type HisF. The resulting recombinant protein HisF-C*C, which was produced in an insoluble form and unfolded with low cooperativity at moderate urea concentrations has now been stabilised and solubilised by a combination of random mutagenesis and selection in vivo. For this purpose, Escherichia coli cells were transformed with a plasmid-based gene library encoding HisF- C*C variants fused to chloramphenicol acetyltransferase (CAT). Stable and soluble variants were identified by the survival of host cells on solid medium containing high concentrations of the antibiotic. The selected HisF- C*C proteins, which were characterised in vitro in the absence of CAT, contained eight different amino acid substitutions. One of the exchanges (Y143C) stabilised HisF-C*C by the formation of an intermolecular disulfide bond. Three of the substitutions (G245R, V248M, L250Q) were located in the long loop connecting the two HisF-C copies, whose subsequent truncation from 13 to 5 residues yielded the stabilised variant HisF-C*C Δ. From the remaining substitutions, Y143H and V234M were most beneficial, and molecular dynamics simulations suggest that they strengthen the interac- tions between the half barrels by establishing a hydrogen-bonding network and an extensive hydrophobic cluster, respectively. By combining the loop deletion of HisF-C*C Δ with the Y143H and V234M substitutions, the variant HisF-C**C was generated. Recombinant HisF-C**C is produced in soluble form, forms a pure monomer with its tryptophan residues shielded from solvent and unfolds with similar cooperativity as HisF. Our results show that, starting from two identical and fused half barrels, few amino acid exchanges are sufficient to generate a highly stable and compact (βα) 8 - barrel protein with wild-type like structural properties. © 2007 Elsevier Ltd. All rights reserved. *Corresponding author Keywords: protein design; enzyme evolution; (βα) 8 -barrel; half barrel; stability screen Introduction It has been suggested that complex contemporary protein folds have evolved by the association and fusion of small polypeptide fragments. 1,2 The in- ternal symmetry observed in a number of enzymes suggests that identical polypeptide segments first assembled to homo-oligomers, followed by the covalent linkage of the fragments as a consequence of gene duplication and fusion. 3–5 The (βα) 8 (or Abbreviations used: AdoMet, S-adenosyl-L-methionine; CAT, chloramphenicol acetyltransferase; MD, molecular dynamics; GdmCl, guanidinium chloride. E-mail address of the corresponding author: Reinhard.Sterner@biologie.uni-regensburg.de doi:10.1016/j.jmb.2007.06.036 J. Mol. Biol. (2007) 372, 114–129 0022-2836/$ - see front matter © 2007 Elsevier Ltd. All rights reserved.