De novo heme proteins from designed combinatorial libraries

Nina R.L. Rojas, Satwik Kamtekar, Cyrena T. Simons, Jeremy E. Mclean, Kathleen M. Vogel, Thomas G. Spiro, Ramy S. Farid, Michael H. Hecht

Research output: Contribution to journalArticle

106 Scopus citations

Abstract

We previously reported the design of a library of de novo amino acid sequences targeted to fold into four-helix bundles. The design of these sequences was based on a 'binary code' strategy, in which the patterning of polar and nonpolar amino acids is specified explicitly, but the exact identities of the side chains is varied extensively (Kamtekar S, Schiffer JM, Xiong H, Babik JM, Hecht MH, 1993, Science 262:1680-1685). Because of this variability, the resulting collection of amino acid sequences may include de novo proteins capable of binding biologically important cofactors. To probe for such binding, the de novo sequences were screened for their ability to bind the heme cofactor. Among an initial collection of 30 binary code sequences, 15 are shown to bind heme and form bright red complexes. Characterization of several of these de novo heme proteins demonstrated that their absorption spectra and resonance Raman spectra resemble those of natural cytochromes. Because the design of these sequences is based on global features of polar/nonpolar patterning, the finding that half of them bind heme highlights the power of the binary code strategy, and demonstrates that isolating de novo heme proteins does not require explicit design of the cofactor binding site. Because bound heme plays a key role in the functions of many natural proteins, these results suggest that binary code sequences may serve as initial prototypes for the development of large collections of functionally active de novo proteins.

Original languageEnglish (US)
Pages (from-to)2512-2524
Number of pages13
JournalProtein Science
Volume6
Issue number12
DOIs
StatePublished - Dec 1997

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology

Keywords

  • Binary code
  • Combinatorial libraries
  • De novo proteins
  • Heme binding
  • Protein design

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    Rojas, N. R. L., Kamtekar, S., Simons, C. T., Mclean, J. E., Vogel, K. M., Spiro, T. G., Farid, R. S., & Hecht, M. H. (1997). De novo heme proteins from designed combinatorial libraries. Protein Science, 6(12), 2512-2524. https://doi.org/10.1002/pro.5560061204