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1. Zn(II) Affinity and Structural Conformations of 2His‐2Cys Zinc Finger‐Like Motif Peptide Determined by Ion Mobility–Mass Spectrometry and PM6 Molecular Modeling

   https://doi.org/10.1002/jms.5113  

   Adomako, Richmond A.; Owusu, Michael B.; Oberdick, Rebekah K.; Senyah, Kwabena; Asare, Perfect; Spezia, Riccardo; Angel, Laurence A. (February 2025, Journal of Mass Spectrometry)

   ABSTRACT This study focuses on investigating the conformational structure and zinc(II) affinity of a zinc finger‐like motif (ZFM) peptide with the sequence acetyl‐His₁‐Cys₂‐Gly₃‐Pro₄‐Gly₅‐His₆‐Cys₇, where bold highlights the potential zinc(II) binding sites. Zinc fingers are crucial protein motifs known for their high specificity and affinity for zinc ions. The ZFM peptide's sequence contains the 2His‐2Cys zinc‐binding sites similar to those in natural zinc finger proteins but without the hydrophobic core, making it a valuable model for studying zinc(II)–peptide interactions. Previous research on related peptides showed that collision cross sections and B3LYP modeling predicted that the His‐2Cys‐carboxyl terminus coordination of zinc(II) was more stable than the 2His‐2Cys. Employing a comprehensive approach integrating ion mobility–mass spectrometry and theoretical modeling techniques, various zinc(II) binding modes of the ZFM have been thoroughly compared to ascertain their influence on the competitive threshold collision‐induced dissociation method for measuring the relative gas‐phase Zn(II) affinity of the ZFM peptide. The measured Zn(II) affinity of ZFM is greater than those measured recently for two peptides with similar primary structures, acetyl‐His₁‐Cys₂‐Gly₃‐Pro₄‐Gly₅‐Gly₆‐Cys₇and acetyl‐Asp₁‐His₂‐Gly₃‐Pro₄‐Gly₅‐Gly₆‐Cys₇, indicating the preference for the His₁‐Cys₂‐His₆‐Cys₇side groups for coordinating zinc(II) over the His‐2Cys‐carboxyl terminus or Asp‐His‐Cys‐carboxyl terminus in these related heptapeptides. 

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2. Synthesis and conformational preferences of peptides and proteins with cysteine sulfonic acid

   https://doi.org/10.1039/D3OB00179B  

   Bhatt, Megh R.; Zondlo, Neal J. (March 2023, Organic & Biomolecular Chemistry)

   Cysteine sulfonic acid (Cys-SO3H; cysteic acid) is an oxidative post-translational modification of cysteine, resulting from further oxidation from cysteine sulfinic acid (Cys- SO2H). Cysteine sulfonic acid is considered an irreversible post-translational modification, which serves as a biomarker of oxidative stress that has resulted in oxidative damage to proteins. Cysteine sulfonic acid is anionic, as a sulfonate (Cys-SO –; cysteate), in the ionization state that 3 is almost exclusively present at physiological pH (pKa ~ –2). In order to understand protein structural changes that can occur upon oxidation to cysteine sulfonic acid, we analyzed its conformational preferences, using experimental methods, bioinformatics, and DFT-based computational analysis. Cysteine sulfonic acid was incorporated into model peptides for α-helix and polyproline II helix (PPII). Within peptides, oxidation of cysteine to the sulfonic acid proceeds rapidly and efficiently at room temperature in solution with methyltrioxorhenium (MeReO3) and H2O2. Peptides containing cysteine sulfonic acid were also generated on solid phase using trityl-protected cysteine and oxidation with MeReO3 and H2O2. Using methoxybenzyl (Mob)-protected cysteine, solid-phase oxidation with MeReO3 and H2O2 generated the Mob sulfone precursor to Cys-SO – within fully synthesized peptides. These two solid-phase methods allow the synthesis of peptides containing either Cys-SO – or Cys-SO – in a 32 practical manner, with no solution-phase synthesis required. Cys-SO – had low PPII propensity 3 for PPII propagation, despite promoting a relatively compact conformation in φ. In contrast, in a PPII initiation model system, Cys-SO – promoted PPII relative to neutral Cys, with PPII initiation similar to Cys thiolate but less than Cys-SO – or Ala. In an α-helix model system, Cys- 2 SO – promoted α-helix near the N-terminus, due to favorable helix dipole interactions and 3 favorable α-helix capping via a sulfonate-amide side chain-main chain hydrogen bond. Across all peptides, the sulfonate side chain was significantly less ordered than that of the sulfinate. Analysis of Cys-SO – in the PDB revealed a very strong propensity for local (i/i or i/i+1) side 3 chain-main chain sulfonate-amide hydrogen bonds for Cys-SO –, with > 80% of Cys-SO – 33 residues exhibiting these interactions. DFT calculations conducted to explore these conformational preferences indicated that side chain-main chain hydrogen bonds of the sulfonate with the intraresidue amide and/or with the i+1 amide were favorable. However, hydrogen bonds to water or to amides, as well as interactions with oxophilic metals, were weaker for the sulfonate than the sulfinate, due to lower charge density on the oxygens in the sulfonate. 

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3. Single-conformation spectroscopy of cold, protonated ^D PG-containing peptides: switching β-turn types and formation of a sequential type II/II′ double β-turn

   https://doi.org/10.1039/D1CP04852J  

   Lawler, John T.; Harrilal, Christopher P.; DeBlase, Andrew F.; Sibert, Edwin L.; McLuckey, Scott A.; Zwier, Timothy S. (January 2022, Physical Chemistry Chemical Physics)

   d -Proline ( D Pro, D P) is widely utilized to form β-hairpin loops in engineered peptides that would otherwise be unstructured, most often as part of a D PG sub-unit that forms a β-turn. To observe whether D PG facilitated this effect in short protonated peptides, conformation specific IR–UV double resonance photofragment spectra of the cold (∼10 K) protonated D P and L P diastereomers of the pentapeptide YAPGA was carried out in the hydride stretch (2800–3700 cm −1 ) and amide I/II (1400–1800 cm −1 ) regions. A model localized Hamiltonian was developed to better describe the 1600–1800 cm −1 region commonly associated with the amide I vibrations. The CO stretch fundamentals experience extensive mixing with the N–H bending fundamentals of the NH 3 + group in these protonated peptides. The model Hamiltonian accounts for experiment in quantitative detail. In the D P diastereomer, all the population is funneled into a single conformer which presented as a type II β-turn with A and D P in the i + 1 and i + 2 positions, respectively. This structure was not the anticipated type II′ β-turn across D PG that we had hypothesized based on solution-phase propensities. Analysis of the conformational energy landscape shows that both steric and charge-induced effects play a role in the preferred formation of the type II β-turn. In contrast, the L P isomer forms three conformations with very different structures, none of which were type II/II′ β-turns, confirming that L PG is not a β-turn former. Finally, single-conformation spectroscopy was also carried out on the extended peptide [YAA D PGAAA + H] + to determine whether moving the protonated N-terminus further from D PG would lead to β-hairpin formation. Despite funneling its entire population into a single peptide backbone structure, the assigned structure is not a β-hairpin, but a concatenated type II/type II′ double β-turn that displaces the peptide backbone laterally by about 7.5 Å, but leaves the backbone oriented in its original direction. 

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4. Donor acceptor fluorophores: synthesis, optical properties, TD-DFT and cytotoxicity studies

   https://doi.org/10.1039/D0OB02313B  

   Essam, Zahraa M.; Ozmen, Guliz Ersoy; Setiawan, Dani; Hamid, Riri Rizkianty; Abd El-Aal, Reda M.; Aneja, Ritu; Hamelberg, Donald; Henary, Maged (March 2021, Organic & Biomolecular Chemistry)

   null (Ed.)

   Donor–π-acceptor (D–π-A) fluorophores consisting of a donor unit, a π linker, and an acceptor moiety have attracted attention in the last decade. In this study, we report the synthesis, characterization, optical properties, TD-DFT, and cytotoxicity studies of 17 near infrared (NIR) D–π-A analogs which have not been reported so far to the best of our knowledge. These fluorophores have chloroacrylic acid as the acceptor unit and various donor units such as indole, benzothiazole, benzo[ e ]indole, and quinoline. The fluorophores showed strong absorption in the NIR (700–970 nm) region due to their enhanced intramolecular charge transfer (ICT) between chloroacrylic acid and the donor moieties connected with the Vilsmeier–Haack linker. The emission wavelength maxima of the fluorophores were in between 798 and 870 nm. Compound 20 with a 4-quinoline donor moiety showed an emission wavelength above 1000 nm in the NIR II window. The synthesized fluorophores were characterized by 1 H NMR and 13 C NMR, and their optical properties were studied. Time dependent density functional theory (TD-DFT) calculations showed that the charge transfer occurs from the donor groups (indole, benzothiazole, benzo[ e ]indole, and quinoline) to the acceptor chloroacrylic acid moiety. Fluorophores with [HOMO] to [LUMO+1] transitions were shown to possess a charge separation character. The cytotoxicity of selected fluorophores, 4 , 7 , 10 and 12 was investigated against breast cancer cell lines and they showed better activity than the anti-cancer agent docetaxel. 

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5. A Cysteine‐Directed Proximity‐Driven Crosslinking Method for Native Peptide Bicyclization

   https://doi.org/10.1002/anie.202306813  

   Chen, Fa‐Jie; Pinnette, Nicole; Yang, Fan; Gao, Jianmin (June 2023, Angewandte Chemie International Edition)

   Abstract Efficient and site‐specific modification of native peptides and proteins is desirable for synthesizing antibody‐drug conjugates as well as for constructing chemically modified peptide libraries using genetically encoded platforms such as phage display. In particular, there is much interest in efficient multicyclization of native peptides due to the appeals of multicyclic peptides as therapeutics. However, conventional approaches for multicyclic peptide synthesis require orthogonal protecting groups or non‐proteinogenic clickable handles. Herein, we report a cysteine‐directed proximity‐driven strategy for the constructing bicyclic peptides from simple natural peptide precursors. This linear to bicycle transformation initiates with rapid cysteine labeling, which then triggers proximity‐driven amine‐selective cyclization. This bicyclization proceeds rapidly under physiologic conditions, yielding bicyclic peptides with a Cys‐Lys‐Cys, Lys‐Cys‐Lys or N‐terminus‐Cys‐Cys stapling pattern. We demonstrate the utility and power of this strategy by constructing bicyclic peptides fused to proteins as well as to the M13 phage, paving the way to phage display of novel bicyclic peptide libraries. 

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