Systematic circular permutation of an entire protein reveals essential folding elements

Abstract

The importance of chain connectivity in determining protein function and stability can be examined by breaking the peptide backbone using a technique such as circular permutation. Cleavage at certain positions results in a complete loss of the ability of the protein to fold. When such cleavage sites occur sequentially in the primary structure, we call the region a ‘folding element’, a new concept that could assist in our understanding of the protein folding problem. The folding elements of dihydrofolate reductase have been assigned by conducting a systematic circular permutation analysis in which the peptide backbone was sequentially broken between every pair of residues in the protein. The positions of folding elements do not appear to correspond to secondary structure motifs, substrate or coenzyme binding sites, or accessible surface area. However, almost all of the amino acid residues known to be involved in early folding events are located within the folding elements.

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Figure 1: Summary of systematic circular permutation experiments.
Figure 2: Mapping of the folding elements onto the structure of DHFR (Protein Data Bank accession code 1RX4)28.
Figure 3: Typical urea induced unfolding transition curves of circular permutants.
Figure 4: NADPH binding to circular permuted variants and wild-type DHFR.
Figure 5: Schematic representation of:

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Acknowledgements

We thank N. Furuya, A. Fujisawa, J. Suzuki and T. Takenawa, National Institute of Bioscience and Human Technology, for protein purification, DNA sequencing, and mass spectrometry measurements. We are grateful to C.R. Matthews and V.F. Smith, the Pennsylvania State University, for continuous discussion and encouragement and critical review of this article. This research was supported in part by the New Energy and Industrial Technology Development Organization (NEDO).

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Correspondence to Masahiro Iwakura.

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Iwakura, M., Nakamura, T., Yamane, C. et al. Systematic circular permutation of an entire protein reveals essential folding elements. Nat Struct Mol Biol 7, 580–585 (2000). https://doi.org/10.1038/76811

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