title: Expanding Anfinsen's principle: contributions of synonymous codon selection to rational protein design.
abstract: Anfinsen's principle asserts that all information required to specify the structure of a protein is encoded in its amino acid sequence. However, during protein synthesis by the ribosome, the N-terminus of the nascent chain can begin to fold before the C-terminus is available. We tested whether this cotranslational folding can alter the folded structure of an encoded protein in vivo, versus the structure formed when refolded in vitro. We designed a fluorescent protein consisting of three half-domains, where the N- and C-terminal half-domains compete with each other to interact with the central half-domain. The outcome of this competition determines the fluorescence properties of the resulting folded structure. Upon refolding after chemical denaturation, this protein produced equimolar amounts of the N- and C-terminal folded structures, respectively. In contrast, translation in Escherichia coli resulted in a 2-fold enhancement in the formation of the N-terminal folded structure. Rare synonymous codon substitutions at the 5' end of the C-terminal half-domain further increased selection for the N-terminal folded structure. These results demonstrate that the rate at which a nascent protein emerges from the ribosome can specify the folded structure of a protein.
authors.affiliation: Department of Chemistry & Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States.
authors.forename: Ian M
authors.initials: IM
authors.lastname: Sander
authors.forename: Julie L
authors.initials: JL
authors.lastname: Chaney
authors.forename: Patricia L
authors.initials: PL
authors.lastname: Clark
mesh_terms: D000595:Amino Acid Sequence; D003062:Codon / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics; D015202:Protein Engineering / Q000379:methods*; D011506:Proteins / Q000737:chemistry / Q000235:genetics*
chemical_list: D003062:Codon; D011506:Proteins