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Evolution-Inspired Computational Design of Symmetric Proteins

  • Arnout R. D. Voet
  • David Simoncini
  • Jeremy R. H. Tame
  • Kam Y. J. Zhang
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1529)

Abstract

Monomeric proteins with a number of identical repeats creating symmetrical structures are potentially very valuable building blocks with a variety of bionanotechnological applications. As such proteins do not occur naturally, the emerging field of computational protein design serves as an excellent tool to create them from nonsymmetrical templates. Existing pseudo-symmetrical proteins are believed to have evolved from oligomeric precursors by duplication and fusion of identical repeats. Here we describe a computational workflow to reverse-engineer this evolutionary process in order to create stable proteins consisting of identical sequence repeats.

Key words

Symmetrical proteins Repeat proteins Rosetta Evolution Ancestral reconstruction Computational protein design 

Notes

Acknowledgements

AV acknowledges RIKEN’s program for Junior Scientists for the FPR fellowship and funding.

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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  • Arnout R. D. Voet
    • 1
  • David Simoncini
    • 2
    • 3
  • Jeremy R. H. Tame
    • 4
  • Kam Y. J. Zhang
    • 5
  1. 1.Laboratory for Biomolecular Modelling and DesignKU LeuvenLeuvenBelgium
  2. 2.Structural Bioinformatics Team, Division of Structural and Synthetic BiologyCenter for Life Science Technologies, RIKENYokohama, KanagawaJapan
  3. 3.MIAT, UR-875, INRACastanet TolosanFrance
  4. 4.Drug Design Laboratory, Graduate School of Medical Life ScienceYokohama City UniversityYokohama, KanagawaJapan
  5. 5.Structural Bioinformatics Team, Division of Structural and Synthetic BiologyCenter for Life Science TechnologiesYokohama, KanagawaJapan

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