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  Potential of fragment recombination for rational design of proteins

Eisenbeis, S., Proffitt, W., Coles, M., Truffault, V., Shanmugaratnam, S., Meiler, J., et al. (2012). Potential of fragment recombination for rational design of proteins. Journal of the American Chemical Society, 134(9), 4019-4022. doi:10.1021/ja211657k.

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 Creators:
Eisenbeis, S1, Author           
Proffitt, W, Author
Coles, M2, 3, Author           
Truffault, V4, Author           
Shanmugaratnam, S1, Author           
Meiler, J, Author
Höcker, B1, Author           
Affiliations:
1Research Group Protein Design, Max Planck Institute for Developmental Biology, Max Planck Society, ou_3384430              
2Transmembrane Signal Transduction Group, Department Protein Evolution, Max Planck Institute for Developmental Biology, Max Planck Society, ou_3477410              
3Department Protein Evolution, Max Planck Institute for Developmental Biology, Max Planck Society, Max-Planck-Ring 5, 72076 Tübingen, DE, ou_3375791              
4Department Biochemistry, Max Planck Institute for Developmental Biology, Max Planck Society, ou_3375718              

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 Abstract: It is hypothesized that protein domains evolved from smaller intrinsically stable subunits via combinatorial assembly. Illegitimate recombination of fragments that encode protein subunits could have quickly led to diversification of protein folds and their functionality. This evolutionary concept presents an attractive strategy to protein engineering, e.g., to create new scaffolds for enzyme design. We previously combined structurally similar parts from two ancient protein folds, the (βα)(8)-barrel and the flavodoxin-like fold. The resulting "hopeful monster" differed significantly from the intended (βα)(8)-barrel fold by an extra β-strand in the core. In this study, we ask what modifications are necessary to form the intended structure and what potential this approach has for the rational design of functional proteins. Guided by computational design, we optimized the interface between the fragments with five targeted mutations yielding a stable, monomeric protein whose predicted structure was verified experimentally. We further tested binding of a phosphorylated compound and detected that some affinity was already present due to an intact phosphate-binding site provided by one fragment. The affinity could be improved quickly to the level of natural proteins by introducing two additional mutations. The study illustrates the potential of recombining protein fragments with unique properties to design new and functional proteins, offering both a possible pathway of protein evolution and a protocol to rapidly engineer proteins for new applications.

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 Dates: 2012-03
 Publication Status: Issued
 Pages: -
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 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1021/ja211657k
PMID: 22329686
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Title: Journal of the American Chemical Society
  Other : JACS
  Abbreviation : J. Am. Chem. Soc.
Source Genre: Journal
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Publ. Info: Washington, DC : American Chemical Society
Pages: - Volume / Issue: 134 (9) Sequence Number: - Start / End Page: 4019 - 4022 Identifier: ISSN: 0002-7863
CoNE: https://pure.mpg.de/cone/journals/resource/954925376870