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In silico design of foldable lasso peptides.

John D M Nguyen1, Gabriel C A da Hora1, Marcus C Mifflin1

  • 1Department of Chemistry, University of Utah, Salt Lake City, Utah.

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Summary

Researchers enhanced the stability of pre-lasso conformations, crucial for synthesizing lasso peptides. Sequence optimization and chemical modifications improved the formation of these unique threaded structures, overcoming synthetic challenges.

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Area of Science:

  • Natural Product Chemistry
  • Biotechnology
  • Computational Chemistry

Background:

  • Lasso peptides are natural products with unique threaded structures, offering high stability.
  • Chemical synthesis typically yields non-threaded isomers due to folding challenges.
  • Understanding and enhancing pre-lasso conformations is key to synthetic access.

Purpose of the Study:

  • To improve the relative stability of pre-lasso conformations for lasso peptide synthesis.
  • To investigate sequence optimization, chemical modification, and disulfide incorporation strategies.
  • To overcome the entropic challenges in forming the lasso peptide structure.

Main Methods:

  • Rosetta fixed backbone design for sequence optimization.
  • Well-tempered metadynamics for enhanced conformational sampling.
  • Analysis of chemical modifications and disulfide cross-linking effects.

Main Results:

  • Designed sequences showed improved pre-lasso stability compared to non-threaded conformations.
  • Chemical modifications, particularly to isopeptide bond residues, increased pre-lasso probability.
  • Disulfide cross-linking initially decreased stability but was beneficial when combined with modifications.

Conclusions:

  • Sequence optimization and specific chemical modifications enhance lasso peptide precursor stability.
  • The findings provide a foundation for developing synthetic routes to lasso peptides.
  • Cooperative effects between chemical modifications and cross-linking offer new design possibilities.