Context-dependent secondary structure formation of a designed protein sequence

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Abstract
PROTEIN secondary structures have been viewed as fundamental building blocks for protein folding, structure and design. Pre-vious studies indicate that the propensities of individual amino acids to form particular secondary structures are the result of a combination of local conformational preferences1,2 and non-local factors3–7. To examine the extent to which non-local factors influence the formation of secondary structural elements, we have designed an 11-amino-acid sequence (dubbed the 'chameleon' sequence) that folds as an α-helix when in one position but as a β-sheet when in another position of the primary sequence of the IgG-binding domain of protein G (GUI). Both proteins, chameleon-α and chameleon-β, are folded into structures similar to native GB1, as judged by several biophysical criteria. Our results demonstrate that non-local interactions can determine the secondary structure of peptide sequences of substantial length. They also support views of protein folding that favour tertiary interactions as dominant determinants of structure (for example, see refs 8,9).