Monitoring peptide tyrosine nitration by spectroscopic methods

Acidobasic equilibria of inubosin derivatives studied by UV-Vis spectroscopy

Inubosin derivatives were suggested as compounds supporting the regeneration of neurons. For practical pharmaceutical applications their physicochemical properties need to be optimized in terms of bioavailability, possible side effects, and efficiency. We focused on four inubosin B derivatives, where acidobasic constants as key players in the biological activity were determined using the UV-Vis spectroscopy. The constants were correlated with the structure on the basis of the Hammett theory. In addition, water-organic solvent equilibria were studied for selected compounds. A software for semi-automated processing of the UV-Vis titration data was developed and tested. Time dependent density functional theory (TDDFT) was used to model and interpret the experimental spectra, which made it possible, for example, to assign the most characteristic cationic band to the S0 → S2 transition. For the acridine acid, both the TDDFT computations and the experimental data indicate that it forms zwitterion in the aqueous solution, whereas it is not dissociated in the organic phase.

Raman Spectra of Amino Acids and Peptides from Machine Learning Polarizabilities

Raman spectroscopy is an important tool in the study of vibrational properties and composition of molecules, peptides, and even proteins. Raman spectra can be simulated based on the change of the electronic polarizability with vibrations, which can nowadays be efficiently obtained via machine learning models trained on first-principles data. However, the transferability of the models trained on small molecules to larger structures is unclear, and direct training on large structures is prohibitively expensive. In this work, we first train two machine learning models to predict the polarizabilities of all 20 amino acids. Both models are carefully benchmarked and compared to density functional theory (DFT) calculations, with the neural network method being found to offer better transferability. By combination of machine learning models with classical force field molecular dynamics, Raman spectra of all amino acids are also obtained and investigated, showing good agreement with experiments. The models are further extended to small peptides. We find that adding structures containing peptide bonds to the training set greatly improves predictions, even for peptides not included in training sets.

Colloidal surface-enhanced Raman spectroscopic study of grouper epidermal mucus using acidified sodium sulphate as the aggregating agent

Fish epidermal mucus is an important reservoir of antipathogenic compounds which serves as the first line of the immune defence. Despite its significant role in the physiology and health of fish, detailed profiling of fish epidermal mucus has yet to be explored. Therefore, this study investigates a label-free colloidal surface-enhanced Raman spectroscopic (SERS) method for profiling grouper mucus. Gold nanoparticles were first synthesised using the standard citrate reduction and characterised using ultraviolet-visible spectroscopy, transmission electron microscopy and dynamic light scattering. The influence of acidified sodium sulphate (Na2SO4) at pH 3 as the aggregating agent on the enhancement of the SERS spectrum of different analyte samples including rhodamine 6G (R6G) dye, lysozyme solution and hybrid grouper (Epinephelus fuscoguttatus × Epinephelus lanceolatus) mucus was observed. Based on the results, an optimal Na2SO4 concentration of 1 M was recorded to achieve the highest enhancement of the SERS signal for R6G and grouper mucus, while the optimal concentration for lysozyme was 0.1 M. The results indicated a higher degree of aggregation induced by lysozyme than R6G and grouper mucus. A few overlapping peaks of the SERS spectra of lysozyme and grouper mucus made it possible to confirm the presence of lysozyme as potential biomarkers.

Conformations and hydration of halopropionic acids studied by molecular dynamics and Raman optical activity

Chiral 2-halopropionic acids and their derivatives were synthesized and their properties studied computationally using Raman and Raman optical activity (ROA) spectroscopy. For neat acids present as liquids small amount of water led to significant changes in the spectra, resulting even to flipping of some ROA band signs. We find this interesting for the role water plays in interpretation of vibrational optical activity spectra of biomolecules. Analysis of the results shows that when the water is present, it can change ROA band signs due to the changes in acidobasic equilibrium. Corresponding esters without acidic hydrogens do not exhibit such effects.

Chiral Monitoring Across Both Enantiomeric Excess and Concentration Space: Leveraging Quantum Cascade Lasers for Sensitive Vibrational Circular Dichroism Spectroscopy

Recently, high-throughput quantum cascade laser-based vibrational circular dichroism (QCL-VCD) technology has reduced the measurement time for high-quality vibrational circular dichroism spectra from hours to a few minutes. This study evaluates QCL-VCD for chiral monitoring using flow-through measurement of a changing sample in a circulating loop. A balanced detection QCL-VCD system was applied to the enantiomeric pair R/S-1,1'-bi-2-naphthol in solution. Different mixtures of the two components were used to simulate a racemization process, collecting spectral data at a time resolution of 6 min, and over three concentration levels. The goal of this experimental setup was to evaluate QCL-VCD in terms of both molar and enantiomeric excess (EE) sensitivity at a time resolution relevant to chiral monitoring in chemical processes. Subsequent chemometric evaluation by partial least squares regression revealed a cross-validated prediction accuracy of 2.8% EE with a robust prediction also for the test data set (error = 3.5% EE). In addition, the data set was also treated with the least absolute shrinkage and selection operator (LASSO), which also achieved a robust prediction. Due to the operating principle of LASSO, the obtained coefficients constituted a few discrete spectral frequencies, which represent the most variance. This information can be used in the future for dedicated QCL-based instrument design, gaining a higher time resolution without sacrificing predictive capabilities.

Size-controllable colloidal Ag nano-aggregates with long-time SERS detection window for on-line high-throughput detection

Making metal nanoparticle aggregates is a common way to improve surface-enhanced Raman scattering (SERS) enhancement via the formation of hot spots between nanoparticles. Here, we propose a "freeze-thaw-ultrasonication" method to obtain stable colloidal Ag nano-aggregates (AgNAs) with controllable sizes, which can remain stable for a few days. Compared with other method using aggregation reagents (e.g., organic molecules and salt), this method can maintain metal surface charges and adsorption affinity, which ensures the excellent SERS stability and sensitivity. The SERS detection window during the experiment can reach more than 25 min, which makes it a prerequisite for accurate SERS detection during a long-time range. Combining the obtained stable AgNAs with microfluidic devices, we established a sequential SERS on-line continuous detection method for the high-throughput detection of multiplex samples. The UV-Fenton degradation process of methylene blue (MB) is continuously on-line monitored through this platform, which is more sensitive than the UV-Vis Spectrum. Moreover, we have realized the sensitive and accurate detection of 5-nitro-8-hydroxyquinoline (5-NQ) with antibacterial and anticancer activities based on chloride-functionalized silver, which paved a way for SERS high-throughput analysis in bioanalysis and other fields.

Raman Fingerprints of the SARS-CoV-2 Delta Variant and Mechanisms of Its Instantaneous Inactivation by Silicon Nitride Bioceramics

Raman spectroscopy uncovered molecular scale markers of the viral structure of the SARS-CoV-2 Delta variant and related viral inactivation mechanisms at the biological interface with silicon nitride (Si3N4) bioceramics. A comparison of Raman spectra collected on the TY11-927 variant (lineage B.1.617.2; simply referred to as the Delta variant henceforth) with those of the JPN/TY/WK-521 variant (lineage B.1.617.1; referred to as the Kappa variant or simply as the Japanese isolate henceforth) revealed the occurrence of key mutations of the spike receptor together with profound structural differences in the molecular structure/symmetry of sulfur-containing amino acid and altered hydrophobic interactions of the tyrosine residue. Additionally, different vibrational fractions of RNA purines and pyrimidines and dissimilar protein secondary structures were also recorded. Despite mutations, hydrolytic reactions at the surface of silicon nitride (Si3N4) bioceramics induced instantaneous inactivation of the Delta variant at the same rate as that of the Kappa variant. Contact between virions and micrometric Si3N4 particles yielded post-translational deimination of arginine spike residues, methionine sulfoxidation, tyrosine nitration, and oxidation of RNA purines to form formamidopyrimidines. Si3N4 bioceramics proved to be a safe and effective inorganic compound for instantaneous environmental sanitation.

Cell penetrating peptide (CPP) gold(iii) - complex - bioconjugates: from chemical design to interaction with cancer cells for nanomedicine applications

This study promotes an innovative synthesis of a nanotheragnostic scaffold capable of targeting and destroying pancreatic cancer cells (PDAC) using the Biotinylated NFL-TBS.40-63 peptide (BIOT-NFL), known to enter various glioblastoma cancer cells (GBM) where it specifically destroys their microtubule network. This recently proposed methodology (P7391FR00-50481 LIV) applied to other peptides VIM (Vimentin) and TAT (Twin-Arginine Translocation) (CPP peptides) has many advantages, such as targeted selective internalization and high stability under experimental conditions, modulated by steric and chemical configurations of peptides. The successful interaction of peptides on gold surfaces has been confirmed by UV-visible, dynamic light scattering (DLS), Zeta potential (ZP) and Raman spectroscopy analyses. The cellular internalization in pancreatic ductal adenocarcinoma (PDAC; MIA PACA-2) and GBM (F98) cells was monitored by transmission electron microscopy (TEM) and showed a better cellular internalization in the presence of peptides with gold nanoparticles. In this work, we also evaluated the power of these hybrid peptide-nanoparticles as photothermal agents after cancer cell internalization. These findings envisage novel perspectives for the development of high peptide-nanotheragnostics.

Photochemical synthesis of pink silver and its use for monitoring peptide nitration via surface enhanced Raman spectroscopy (SERS)

Oxidative stress may cause extended tyrosine posttranslational modifications of peptides and proteins. The 3-nitro-L-tyrosine (Nit), which is typically formed, affects protein behavior during neurodegenerative processes, such as Alzheimer's and Parkinson's diseases. Such metabolic products may be conveniently detected at very low concentrations by surface enhanced Raman spectroscopy (SERS). Previously, we have explored the SERS detection of the Nit NO₂ bending vibrational bands in a presence of hydrogen chloride (Niederhafner et al., Amino Acids 53:517-532, 2021, ibid). In this article, we describe performance of a new SERS substrate, "pink silver", synthesized photochemically. It provides SERS even without the HCl induction, and the acid further decreases the detection limit about 9 times. Strong SERS bands were observed in the asymmetric (1550-1475 cm^-1) and symmetric (1360-1290 cm^-1) NO stretching in the NO₂ group. The bending vibration was relatively weak, but appeared stronger when HCl was added. The band assignments were supported by density functional theory modeling.

Protein Tyrosine Nitration in Plant Nitric Oxide Signaling

Nitric oxide (NO), which is ubiquitously present in living organisms, regulates many developmental and stress-activated processes in plants. Regulatory effects exerted by NO lies mostly in its chemical reactivity as a free radical. Proteins are main targets of NO action as several amino acids can undergo NO-related post-translational modifications (PTMs) that include mainly S-nitrosylation of cysteine, and nitration of tyrosine and tryptophan. This review is focused on the role of protein tyrosine nitration on NO signaling, making emphasis on the production of NO and peroxynitrite, which is the main physiological nitrating agent; the main metabolic and signaling pathways targeted by protein nitration; and the past, present, and future of methodological and strategic approaches to study this PTM. Available information on identification of nitrated plant proteins, the corresponding nitration sites, and the functional effects on the modified proteins will be summarized. However, due to the low proportion of in vivo nitrated peptides and their inherent instability, the identification of nitration sites by proteomic analyses is a difficult task. Artificial nitration procedures are likely not the best strategy for nitration site identification due to the lack of specificity. An alternative to get artificial site-specific nitration comes from the application of genetic code expansion technologies based on the use of orthogonal aminoacyl-tRNA synthetase/tRNA pairs engineered for specific noncanonical amino acids. This strategy permits the programmable site-specific installation of genetically encoded 3-nitrotyrosine sites in proteins expressed in Escherichia coli, thus allowing the study of the effects of specific site nitration on protein structure and function.

Mechanisms of instantaneous inactivation of SARS-CoV-2 by silicon nitride bioceramic

The hydrolytic processes occurring at the surface of silicon nitride (Si3N4) bioceramic have been indicated as a powerful pathway to instantaneous inactivation of SARS-CoV-2 virus. However, the virus inactivation mechanisms promoted by Si3N4 remain yet to be elucidated. In this study, we provide evidence of the instantaneous damage incurred on the SARS-CoV-2 virus upon contact with Si3N4. We also emphasize the safety characteristics of Si3N4 for mammalian cells. Contact between the virions and micrometric Si3N4 particles immediately targeted a variety of viral molecules by inducing post-translational oxidative modifications of S-containing amino acids, nitration of the tyrosine residue in the spike receptor binding domain, and oxidation of RNA purines to form formamidopyrimidine. This structural damage in turn led to a reshuffling of the protein secondary structure. These clear fingerprints of viral structure modifications were linked to inhibition of viral functionality and infectivity. This study validates the notion that Si3N4 bioceramic is a safe and effective antiviral compound; and a primary antiviral candidate to replace the toxic and allergenic compounds presently used in contact with the human body and in long-term environmental sanitation.

Chiral detection by induced surface-enhanced Raman optical activity

Combination of optical activity with surface-enhanced Raman scattering has been a dream of physical chemists for a long time. We report a measurement protocol based on silver colloids and aromatic linkers where chiral acids could be detected in concentrations of about 10-5 M. We explain the mechanism by binding and self-assembly of the linkers into chiral aggregates on the silver surface. Following the "sergeants-and-soldiers" principle, the chirality is determined by the relatively minor acidic component. Such detection of biologically relevant molecules may be useful when other methods, such as electronic circular dichroism, are not sensitive enough. In the future, variations of the chemical structure of the linker or other conditions are needed to provide a more specific signal allowing one to better discriminate among the optically active molecules.