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Abstract Peptide‐protein docking is challenging due to the considerable conformational freedom of the peptide. CAPRI rounds 38‐45 included two peptide‐protein interactions, both characterized by a peptide forming an additional beta strand of a beta sheet in the receptor. Using theRosetta FlexPepDockpeptide docking protocol we generated top‐performing, high‐accuracy models for targets 134 and 135, involving an interaction between a peptide derived from L‐MAG with DLC8. In addition, we were able to generate the only medium‐accuracy models for a particularly challenging target, T121. In contrast to the classical peptide‐mediated interaction, in which receptor side chains contact both peptide backbone and side chains, beta‐sheet complementation involves a major contribution to binding by hydrogen bonds between main chain atoms. To establish how binding affinity and specificity are established in this special class of peptide‐protein interactions, we extractedPeptiDBeta, a benchmark of solved structures of different protein domains that are bound by peptides via beta‐sheet complementation, and tested our protocol for global peptide‐dockingPIPER‐FlexPepDockon this dataset. We find that the beta‐strand part of the peptide is sufficient to generate approximate and even high resolution models of many interactions, but inclusion of adjacent motif residues often provides additional information necessary to achieve high resolution model quality.
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This content will become publicly available on December 16, 2025
Discovery and Heterologous Expression of Trilenodin, an Antimicrobial Lasso Peptide with a Unique Tri‐Isoleucine Motif
Abstract Lasso peptides are an increasingly relevant class of peptide natural products with diverse biological activities, intriguing physical properties, and unique chemical structures. Most characterized lasso peptides have been from Actinobacteria and Proteobacteria, despite bioinformatic analyses suggesting that other bacterial taxa, particularly those from Firmicutes, are rich in biosynthetic gene clusters (BGCs) encoding lasso peptides. Herein, we report the bioinformatic identification of a lasso peptide BGC fromPaenibacillus taiwanensisDSM18679 which we termedpats. We used a bioinformatics‐guided isolation approach and high‐resolution tandem mass spectrometry (HRMS/MS) to isolate and subsequently characterize a new lasso peptide produced from thepatsBGC, which we named trilenodin, after the tri‐isoleucine motif present in its primary sequence. This tri‐isoleucine motif is unique among currently characterized lasso peptides. We confirmed the connection between thepatsBGC and trilenodin production by establishing the firstBacillus subtilis168‐based heterologous expression system for expressing Firmicutes lasso peptides. We finally determined that trilenodin exhibits potent antimicrobial activity againstB. subtilisandKlebsiella pneumoniae, making trilenodin the first characterized biologically active lasso peptide from Firmicutes. Collectively, we demonstrate that bacteria from Firmicutes can serve as high‐potential sources of chemically and biologically diverse lasso peptides.
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- Award ID(s):
- 2216137
- PAR ID:
- 10640558
- Publisher / Repository:
- European Chemistry Societies
- Date Published:
- Journal Name:
- ChemBioChem
- Volume:
- 25
- Issue:
- 24
- ISSN:
- 1439-4227
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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