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Accessing Transient Binding Pockets by Protein Engineering and Yeast Surface Display Screening

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Genotype Phenotype Coupling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2681))

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Abstract

The binding pocket of some therapeutic targets can acquire multiple conformations that, to some extent, depend on the protein dynamics and the interaction with other molecules. The inability to reach the binding pocket can impose a substantial or even insurmountable barrier for the de novo identification or optimization of small-molecule ligands. Herein, we describe a protocol for the engineering of a target protein and a yeast display FACS sorting strategy to identify protein variants with a stable transient binding pocket with improved binding for a cryptic site-specific ligand. This strategy may facilitate drug discovery using the resulting protein variants with accessible binding pockets for ligand screening.

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Author information

Authors and Affiliations

  1. Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany

    Jorge A. Lerma Romero & Harald Kolmar

  2. Centre for Synthetic Biology, Technical University of Darmstadt, Darmstadt, Germany

    Harald Kolmar

Authors
  1. Jorge A. Lerma Romero
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  2. Harald Kolmar
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Corresponding author

Correspondence to Harald Kolmar .

Editor information

Editors and Affiliations

  1. Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany

    Stefan Zielonka

  2. Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany

    Simon Krah

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Lerma Romero, J.A., Kolmar, H. (2023). Accessing Transient Binding Pockets by Protein Engineering and Yeast Surface Display Screening. In: Zielonka, S., Krah, S. (eds) Genotype Phenotype Coupling. Methods in Molecular Biology, vol 2681. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3279-6_14

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  • DOI: https://doi.org/10.1007/978-1-0716-3279-6_14

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3278-9

  • Online ISBN: 978-1-0716-3279-6

  • eBook Packages: Springer Protocols

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