Novel folded protein domains generated by combinatorial shuffling of polypeptide segments.
It has been proposed that the architecture of protein domains has evolved by the combinatorial assembly and/or exchange of smaller polypeptide segments. To investigate this proposal, we fused DNA encoding the N-terminal half of a beta-barrel domain (from cold shock protein CspA) with fragmented genomic Escherichia coli DNA and cloned the repertoire of chimeric polypeptides for display on filamentous bacteriophage. Phage displaying folded polypeptides were selected by proteolysis; in most cases the protease-resistant chimeric polypeptides comprised genomic segments in their natural reading frames. Although the genomic segments appeared to have no sequence homologies with CspA, one of the originating proteins had the same fold as CspA, but another had a different fold. Four of the chimeric proteins were expressed as soluble polypeptides; they formed monomers and exhibited cooperative unfolding. Indeed, one of the chimeric proteins contained a set of very slowly exchanging amides and proved more stable than CspA itself. These results indicate that native-like proteins can be generated directly by combinatorial segment assembly from nonhomologous proteins, with implications for theories of the evolution of new protein folds, as well as providing a means of creating novel domains and architectures in vitro.
Riechmann
L
L
Division for Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom.
Winter
G
G
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D002151:Calorimetry; D020650:Combinatorial Chemistry Techniques; D004926:Escherichia coli / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019151:Peptide Library; D011489:Protein Denaturation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D011993:Recombinant Fusion Proteins / Q000737:chemistry; D012260:Ribonucleases / Q000737:chemistry*; D013816:Thermodynamics
D001426:Bacterial Proteins; D019151:Peptide Library; D011506:Proteins; D011993:Recombinant Fusion Proteins; C062260:cold shock protein CS7.4, Bacteria; D012260:Ribonucleases; C019760:Bacillus amyloliquefaciens ribonuclease