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Designed leucine-rich repeat proteins bind two muramyl dipeptide ligands.

Christina S Kim1, Anne M Brown2, Tijana Z Grove1

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|January 29, 2021
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Summary

We designed novel consensus leucine-rich repeat proteins (CLRR4-8) that bind bacterial muramyl dipeptide (MDP) with high affinity. These proteins show potential for developing advanced pathogen biosensors.

Keywords:
consensus leucine-rich repeat (CLRR)molecular docking modelmuramyl dipeptide (MDP)nucleotide-binding oligomerization domain (NOD)protein design

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Area of Science:

  • Protein Engineering
  • Immunology
  • Biochemistry

Background:

  • Designed protein receptors offer potential for diagnostics and therapeutics.
  • Nucleotide-binding oligomerization domain (NOD)-like receptors are key in innate immunity.
  • Muramyl dipeptide (MDP) is a critical component of bacterial cell walls.

Purpose of the Study:

  • To design novel consensus leucine-rich repeat proteins (CLRR4-8).
  • To investigate the binding affinity and capacity of these CLRRs for MDP.
  • To explore the potential of CLRRs as scaffolds for pathogen biosensors.

Main Methods:

  • Protein design based on NOD-like receptor LRR domains.
  • Fluorescence quenching experiments to measure binding affinity (Kd app, Kd1, Kd2).
  • Molecular docking studies to analyze MDP binding modes.

Main Results:

  • Five CLRRs (CLRR4-8) were successfully designed.
  • CLRRs exhibited micromolar affinity for MDP, with Kd app values from 1.0 to 57 μM.
  • Biphasic binding curves indicated high-capacity binding, with Kd1 values from 0.04 to 4.5 μM and Kd2 from 3.1 to 227 μM, suggesting dual MDP binding.

Conclusions:

  • Designed CLRRs demonstrate high-capacity binding of MDP, exceeding previously reported single-binding.
  • The small, soluble, and stable CLRR scaffolds are promising for future pathogen biosensor development.
  • This work advances protein engineering for innate immune system components and biosensing applications.