Synthesis of Fluorescent Dansyl Derivatives of Methoxyamine and Diphenylhydrazine as Free Radical Precursors

Library Screening, In Vivo Confirmation, and Structural and Bioinformatic Analysis of Pentapeptide Sequences as Substrates for Protein Farnesyltransferase

Protein farnesylation is a post-translational modification where a 15-carbon farnesyl isoprenoid is appended to the C-terminal end of a protein by farnesyltransferase (FTase). This process often causes proteins to associate with the membrane and participate in signal transduction pathways. The most common substrates of FTase are proteins that have C-terminal tetrapeptide CaaX box sequences where the cysteine is the site of modification. However, recent work has shown that five amino acid sequences can also be recognized, including the pentapeptides CMIIM and CSLMQ. In this work, peptide libraries were initially used to systematically vary the residues in those two parental sequences using an assay based on Matrix Assisted Laser Desorption Ionization-Mass Spectrometry (MALDI-MS). In addition, 192 pentapeptide sequences from the human proteome were screened using that assay to discover additional extended CaaaX-box motifs. Selected hits from that screening effort were rescreened using an in vivo yeast reporter protein assay. The X-ray crystal structure of CMIIM bound to FTase was also solved, showing that the C-terminal tripeptide of that sequence interacted with the enzyme in a similar manner as the C-terminal tripeptide of CVVM, suggesting that the tripeptide comprises a common structural element for substrate recognition in both tetrapeptide and pentapeptide sequences. Molecular dynamics simulation of CMIIM bound to FTase further shed light on the molecular interactions involved, showing that a putative catalytically competent Zn(II)-thiolate species was able to form. Bioinformatic predictions of tetrapeptide (CaaX-box) reactivity correlated well with the reactivity of pentapeptides obtained from in vivo analysis, reinforcing the importance of the C-terminal tripeptide motif. This analysis provides a structural framework for understanding the reactivity of extended CaaaX-box motifs and a method that may be useful for predicting the reactivity of additional FTase substrates bearing CaaaX-box sequences.

Heterobifunctional Cross-Linker with Dinitroimidazole and N-Hydroxysuccinimide Ester Motifs for Protein Functionalization and Cysteine-Lysine Peptide Stapling

A heterobifunctional cross-linker with one sulfhydryl-reactive dinitroimidazole end and another amine-reactive N-hydroxysuccinimide (NHS) ester end was designed and synthesized. The two motifs of this cross-linker, dinitroimidazole and NHS ester, proved to react with thiol and amine, respectively, in an orthogonal way. The cross-linker was further applied to construct stapled peptides of different sizes and mono- and dual functionalization (including biotinylation, PEGylation, and fluorescence labeling) of protein.

Energetically More Stable Singlet Cyclopentane-1,3-diyl Diradical with π-Single Bonding Character than the Corresponding σ-Single Bonded Compound

Carbon-carbon σ-single bonds are crucial for constructing molecules like ethane derivatives (R3C-CR3), which are composed of tetrahedral four-coordinate carbons. Molecular functions, such as light absorption or emission, originate from the π-bonds existing in ethylene derivatives (R2C═CR2). In this study, a relatively stable cyclopentane-1,3-diyl species with π-single bonding system (C-π-C) with planar four-coordinate carbons is constructed. This diradicaloid is energetically more stable than the corresponding σ-single bonding system. The π-electron single bonding system provides deeper insights into the chemical bonding and the physical properties derived from the small energy gaps between the bonding and antibonding molecular orbitals.

Experimental and Computational Studies on the Interaction of a Dansyl-Based Fluorescent Schiff Base Ligand with Cu2+ Ions and CuO NPs

We studied the interaction of Cu²⁺ ions and CuO nanoparticles with the fluorescent Schiff base ligand H₃L, which derives from the condensation of 4-formyl-3-hydroxybenzoic acid with N-(2-aminobenzyl)-5-(dimethylamino)naphthalene-1-sulfonamide (DsA). A detailed assignment of the most significant bands of the electronic and infrared spectra of H₃L and DsA was performed using DFT methods, based on both crystal structures. The affinity of H₃L to react with Cu²⁺ ions in solution (K_B = 9.01 10³ L mol⁻¹) is similar to that found for the Cu²⁺ ions present on the surface of CuO NPs (K_B = 9.84 10³ L mol⁻¹). Fluorescence spectroscopic measurements suggest five binding sites for H₃L on the surface of the CuO NPs used. The µ-XRF analysis indicates that a polycrystalline sample of CuO-H₃L NPs contains 15:1 Cu:S molar ratio (CuO:H₃L). ATR-FTIR spectroscopy, supported by DFT calculations, showed that the HL²⁻ (as a phenolate and sulfonamide anion) is coordinated to superficial Cu²⁺ ions of the CuO NPs through their azomethine, sulphonamide, and phenolic groups. A solution of H₃L (126 ppb) shows sensitive responses to CuO NPs, with a limit of detection (LOD) of 330 ppb. The working range for detection of CuO NPs with [H₃L] = 126 ppb was 1.1–9.5 ppm. Common metal ions in water, such as Na⁺, K⁺, Mg²⁺, Ca²⁺, Fe³⁺, and Al³⁺ species, do not interfere significantly with the detection of CuO NPs.

The Physical Chemistry and Chemical Physics (PCCP) Section of the International Journal of Molecular Sciences in Its Publications: The First 300 Thematic Articles in the First 3 Years

The Physical Chemistry and Chemical Physics Section (PCCP Section) is one of the youngest among the sections of the International Journal of Molecular Sciences (IJMS)—the year 2021 will only mark three years since its inception [...]