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1. A High‐Throughput Absolute Quantification of Protein‐Bound Tryptophan from Model and Crop Seeds

   https://doi.org/10.1002/cpz1.862  

   Ansaf, Huda; Yobi, Abou; Angelovici, Ruthie (August 2023, Current Protocols)

   Abstract This protocol describes a high‐throughput absolute quantification protocol for the aromatic essential amino acid, tryptophan (Trp). This procedure consists of a milligram‐scale alkaline hydrolysis followed by an absolute quantification step using a multiple reaction monitoring tandem mass spectrometric (LC‐MS/MS) detection method. The approach facilitates the analysis of a few hundred samples per week by using a 96‐well plate extraction setup. Importantly, the method uses only ∼4 mg of tissue per sample and uses the common alkaline hydrolysis protocol, followed by water extraction that includes L ‐Trp‐d5 as an internal standard to enable the quantification of the absolute level of the bound Trp with high precision, accuracy, and reproducibility. The protocol described herein has been optimized for seed samples for Arabidopsis thaliana , Glycine max , and Zea mays but could be applied to other plant tissues. © 2023 Wiley Periodicals LLC. Basic Protocol : Analysis of protein‐bound tryptophan from seeds 

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2. Sulfur isotope analysis of cysteine and methionine via preparatory liquid chromatography and elemental analyzer isotope ratio mass spectrometry

   https://doi.org/10.1002/rcm.9007  

   Phillips, Alexandra_A; Wu, Fenfang; Sessions, Alex_L (January 2021, Rapid Communications in Mass Spectrometry)

   RationaleSulfur isotope analysis of organic sulfur‐containing molecules has previously been hindered by challenging preparatory chemistry and analytical requirements for large sample sizes. The natural‐abundance sulfur isotopic compositions of the sulfur‐containing amino acids, cysteine and methionine, have therefore not yet been investigated despite potential utility in biomedicine, ecology, oceanography, biogeochemistry, and other fields. MethodsCysteine and methionine were subjected to hot acid hydrolysis followed by quantitative oxidation in performic acid to yield cysteic acid and methionine sulfone. These stable, oxidized products were then separated by reversed‐phase high‐performance liquid chromatography (HPLC) and verified via offline liquid chromatography/mass spectrometry (LC/MS). The sulfur isotope ratios (δ³⁴S values) of purified analytes were then measured via combustion elemental analyzer coupled to isotope ratio mass spectrometry (EA/IRMS). The EA was equipped with a temperature‐ramped chromatographic column and programmable helium carrier flow rates. ResultsOn‐column focusing of SO₂in the EA/IRMS system, combined with reduced He carrier flow during elution, greatly improved sensitivity, allowing precise (0.1–0.3‰ 1 s.d.) δ³⁴S measurements of 1 to 10 μg sulfur. We validated that our method for purification of cysteine and methionine was negligibly fractionating using amino acid and protein standards. Proof‐of‐concept measurements of fish muscle tissue and bacteria demonstrated differences up to 4‰ between the δ³⁴S values of cysteine and methionine that can be connected to biosynthetic pathways. ConclusionsWe have developed a sensitive, precise method for measuring the natural‐abundance sulfur isotopic compositions of cysteine and methionine isolated from biological samples. This capability opens up diverse applications of sulfur isotopes in amino acids and proteins, from use as a tracer in organisms and the environment, to fundamental aspects of metabolism and biosynthesis. 

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3. 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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4. Oxidation of Amino Acids by Peracetic Acid: Reaction Kinetics, Pathways and Theoretical Calculations

   https://doi.org/https://doi.org/10.1016/j.wroa.2018.09.002  

   Du, P.; Liu, W.; Cao, H.; Zhao, H.; Huang, C.-H. (January 2018, Water research. X)

   Peracetic acid (PAA) is a sanitizer with increasing use in food, medical and water treatment industries. Amino acids are important components in targeted foods for PAA treatment and ubiquitous in natural waterbodies and wastewater effluents as the primary form of dissolved organic nitrogen. To better understand the possible reactions, this work investigated the reaction kinetics and transformation pathways of selected amino acids towards PAA. Experimental results demonstrated that most amino acids showed sluggish reactivity to PAA except cysteine (CYS), methionine (MET), and histidine (HIS). CYS showed the highest reactivity with a very rapid reaction rate. Reactions of MET and HIS with PAA followed second-order kinetics with rate constants of 4.6 ± 0.2, and 1.8 ± 0.1 M−1s−1 at pH 7, respectively. The reactions were faster at pH 5 and 7 than at pH 9 due to PAA speciation. Low concentrations of H2O2 coexistent with PAA contributed little to the oxidation of amino acids. The primary oxidation products of amino acids with PAA were [O] addition compounds on the reactive sites at thiol, thioether and imidazole groups. Theoretical calculations were applied to predict the reactivity and regioselectivity of PAA electrophilic attacks on amino acids and improved mechanistic understanding. As an oxidative disinfectant, the reaction of PAA with organics to form byproducts is inevitable; however, this study shows that PAA exhibits lower and more selective reactivity towards biomolecules such as amino acids than other common disinfectants, causing less concern of toxic disinfection byproducts. This attribute may allow greater stability and more targeted actions of PAA in various applications. 

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5. The Functional Significance of High Cysteine Content in Eye Lens γ-Crystallins

   https://doi.org/10.3390/biom14050594  

   Serebryany, Eugene; Martin, Rachel W; Takahashi, Gemma R (May 2024, Biomolecules)

   Cataract disease is strongly associated with progressively accumulating oxidative damage to the extremely long-lived crystallin proteins of the lens. Cysteine oxidation affects crystallin folding, interactions, and light-scattering aggregation especially strongly due to the formation of disulfide bridges. Minimizing crystallin aggregation is crucial for lifelong lens transparency, so one might expect the ubiquitous lens crystallin superfamilies (α and βγ) to contain little cysteine. Yet, the Cys content of γ-crystallins is well above the average for human proteins. We review literature relevant to this longstanding puzzle and take advantage of expanding genomic databases and improved machine learning tools for protein structure prediction to investigate it further. We observe remarkably low Cys conservation in the βγ-crystallin superfamily; however, in γ-crystallin, the spatial positioning of Cys residues is clearly fine-tuned by evolution. We propose that the requirements of long-term lens transparency and high lens optical power impose competing evolutionary pressures on lens βγ-crystallins, leading to distinct adaptations: high Cys content in γ-crystallins but low in βB-crystallins. Aquatic species need more powerful lenses than terrestrial ones, which explains the high methionine content of many fish γ- (and even β-) crystallins. Finally, we discuss synergies between sulfur-containing and aromatic residues in crystallins and suggest future experimental directions. 

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