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1. A Tag‐Free Platform for Synthesis and Screening of Cyclic Peptide Libraries

   https://doi.org/10.1002/anie.202320045  

   Bruce, Angele; Adebomi, Victor; Czabala, Patrick; Palmer, Jonathan; McFadden, William_M; Lorson, Zachary_C; Slack, Ryan_L; Bhardwaj, Gaurav; Sarafianos, Stefan_G; Raj, Monika (April 2024, Angewandte Chemie International Edition)

   Abstract In the realm of high‐throughput screening (HTS), macrocyclic peptide libraries traditionally necessitate decoding tags, essential for both library synthesis and identifying hit peptide sequences post‐screening. Our innovation introduces a tag‐free technology platform for synthesizing cyclic peptide libraries in solution and facilitates screening against biological targets to identify peptide binders through unconventional intramolecular CyClick and DeClick chemistries (CCDC) discovered through our research. This combination allows for the synthesis of diverse cyclic peptide libraries, the incorporation of various amino acids, and facile linearization and decoding of cyclic peptide binder sequences. Our sensitivity‐enhancing derivatization method, utilized in tandem with nano LC‐MS/MS, enables the sequencing of peptides even at exceedingly low picomolar concentrations. Employing our technology platform, we have successfully unearthed novel cyclic peptide binders against a monoclonal antibody and the first cyclic peptide binder of HIV capsid protein responsible for viral infections as validated by microscale thermal shift assays (TSA), biolayer interferometry (BLI) and functional assays. 

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2. Modeling beta‐sheet peptide‐protein interactions: Rosetta FlexPepDock in CAPRI rounds 38‐45

   https://doi.org/10.1002/prot.25871  

   Khramushin, Alisa; Marcu, Orly; Alam, Nawsad; Shimony, Orly; Padhorny, Dzmitry; Brini, Emiliano; Dill, Ken A.; Vajda, Sandor; Kozakov, Dima; Schueler‐Furman, Ora (January 2020, Proteins: Structure, Function, and Bioinformatics)

   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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3. Charge guides pathway selection in β-sheet fibrillizing peptide co-assembly

   https://doi.org/10.1038/s42004-020-00414-w  

   Seroski, Dillon T.; Dong, Xin; Wong, Kong M.; Liu, Renjie; Shao, Qing; Paravastu, Anant K.; Hall, Carol K.; Hudalla, Gregory A. (November 2020, Communications Chemistry)

   Abstract Peptide co-assembly is attractive for creating biomaterials with new forms and functions. Emergence of these properties depends on the peptide content of the final assembled structure, which is difficult to predict in multicomponent systems. Here using experiments and simulations we show that charge governs content by affecting propensity for self- and co-association in binary CATCH(+/−) peptide systems. Equimolar mixtures of CATCH(2+/2−), CATCH(4+/4−), and CATCH(6+/6−) formed two-component β-sheets. Solid-state NMR suggested the cationic peptide predominated in the final assemblies. The cationic-to-anionic peptide ratio decreased with increasing charge. CATCH(2+) formed β-sheets when alone, whereas the other peptides remained unassembled. Fibrillization rate increased with peptide charge. The zwitterionic CATCH parent peptide, “Q11”, assembled slowly and only at decreased simulation temperature. These results demonstrate that increasing charge draws complementary peptides together faster, favoring co-assembly, while like-charged molecules repel. We foresee these insights enabling development of co-assembled peptide biomaterials with defined content and predictable properties. 

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4. Fluorinated peptide biomaterials

   https://doi.org/10.1002/pep2.24184  

   Sloand, Janna N.; Miller, Michael A.; Medina, Scott H. (July 2020, Peptide Science)

   Abstract Fluorinated compounds, while rarely used by nature, are emerging as fundamental ingredients in biomedical research, with applications in drug discovery, metabolomics, biospectroscopy, and, as the focus of this review, peptide/protein engineering. Leveraging the fluorous effect to direct peptide assembly has evolved an entirely new class of organofluorine building blocks from which unique and bioactive materials can be constructed. Here, we discuss three distinct peptide fluorination strategies used to design and induce peptide assembly into nano‐, micro‐, and macro‐supramolecular states that potentiate high‐ordered organization into material scaffolds. These fluorine‐tailored peptide assemblies employ the unique fluorous environment to boost biofunctionality for a broad range of applications, from drug delivery to antibacterial coatings. This review provides foundational tactics for peptide fluorination and discusses the utility of these fluorous‐directed hierarchical structures as material platforms in diverse biomedical applications. 

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5. Mechanism of Cationic Peptide‐Induced Assembly of Gold Nanoparticles: Modulation of Electrostatic Repulsion

   https://doi.org/10.1002/agt2.70043  

   Lam, Benjamin; Ramji, Robert; Mullooly, Margaret; Closser, Kristina_D; Pascal, Tod_A; Jokerst, Jesse_V (April 2025, Aggregate)

   ABSTRACT The aggregation of plasmonic nanoparticles can lead to new and controllable properties useful for numerous applications. We recently showed the reversible aggregation of gold nanoparticles (AuNPs) via a small, cationic di‐arginine peptide; however, the mechanism underlying this aggregation is not yet comprehensively understood. Here, we seek insights into the intermolecular interactions of cationic peptide‐induced assembly of citrate‐capped AuNPs by empirically measuring how peptide identity impacts AuNP aggregation. We examined the nanoscale interactions between the peptides and the AuNPs via UV‐vis spectroscopy to determine the structure‐function relationship of peptide length and charge on AuNP aggregation. Careful tuning of the sequence of the di‐arginine peptide demonstrated that the mechanism of assembly is driven by a reduction in electrostatic repulsion. We show that acetylated N‐terminals and carboxylic acid C‐terminals decrease the effectiveness of the peptide in inducing AuNP aggregation. The increase in peptide size through the addition of glycine or proline units hinders aggregation and leads to less redshift. Arginine‐based peptides were also found to be more effective in assembling the AuNPs than cysteine‐based peptides of equivalent length. We also illustrate that aggregation is independent of peptide stereochemistry. Finally, we demonstrate the modulation of peptide‐AuNP behavior through changes to the pH, salt concentration, and temperature. Notably, histidine‐based and tyrosine‐based peptides could reversibly aggregate the AuNPs in response to the pH. 

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