Takashi Nakazawa

Isoaspartic acid (isoAsp) is a common protein modification that spontaneously arises from asparagine or aspartic acid and has been linked to various diseases and health conditions. However, current methods for identifying isoAsp sites in proteins often suffer from ambiguity and have not gained widespread adoption. We developed a novel method that exclusively labels isoAsp with deuterium. This method capitalizes on the unique structural characteristics of isoAsp residues, which possess a free α-carboxyl group and can form an oxazolone ring. Once the oxazolone ring forms, it facilitates racemization at the C^α-position, incorporating a deuteron from a D₂O solvent. The sites of deuterium-incorporated isoAsp in proteins can be unequivocally determined by comparing the precursor and product ion masses of the peptides from proteins reacted in H₂O and D₂O. The effectiveness of this method has been demonstrated through its application to model proteins lysozyme and rituximab. Furthermore, we have confirmed that the isoAsp deuterium-labeling reaction efficiently labels both l- and d-isoAsp without distinction, as well as isoglutamic acid (isoGlu), for which no effective detection methods currently exist.

Isoaspartic acid (isoAsp) is a common protein modification that spontaneously arises from asparagine or aspartic acid, and it has been linked to various diseases and health conditions. However, current methods for identifying isoAsp sites in proteins often suffer from ambiguity and have not gained widespread adoption. We have developed a novel method that exclusively labels isoAsp with deuterium. This method capitalizes on the unique structural characteristics of isoAsp residues, which possess a free α-carboxyl group and can form an oxazolone ring. Once the oxazolone ring forms, it facilitates racemization at the Cα-position, incorporating a deuteron from a D2O solvent. The sites of deuterium-incorporated isoAsp in proteins can be unequivocally determined by comparing the precursor and product ion masses of the peptides from proteins reacted in H2O and D2O. The effectiveness of this method has been demonstrated through its application to model proteins, lysozyme and rituximab. Furthermore, we have confirmed that the isoAsp deuterium labeling reaction efficiently labels both L- and D-isoAsp without distinction, as well as isoglutamic acid (isoGlu), for which no effective detection methods currently exist.

Histidine residues play crucial roles in shaping the function and structure of proteins due to their unique ability to act as both acids and bases. In other words, they can serve as proton donors and acceptors at physiological pH. This exceptional property is attributed to the side-chain imidazole ring of histidine residues. Consequently, determining the acid-base dissociation constant (Ka) of histidine imidazole rings in proteins often yields valuable insights into protein functions. Significant efforts have been dedicated to measuring the pKa values of histidine residues in various proteins, with nuclear magnetic resonance (NMR) spectroscopy being the most commonly used technique. However, NMR-based methods encounter challenges in assigning signals to individual imidazole rings and require a substantial amount of proteins. To address these issues associated with NMR-based approaches, a mass-spectrometry-based method known as histidine hydrogen–deuterium exchange mass spectrometry (His-HDX-MS) has been developed. This technique not only determines the pKa values of histidine imidazole groups but also quantifies their solvent accessibility. His-HDX-MS has proven effective across diverse proteins, showcasing its utility. This review aims to clarify the fundamental principles of His-HDX-MS, detail the experimental workflow, explain data analysis procedures and provide guidance for interpreting the obtained results.

Since 2004, scientific research on the damaged Giant Buddha statues and Buddhist paintings in Bamiyan, Afghanistan, has been conducted at various laboratories and large-scale facilities using mass-spectrometry techniques (GC-MS, LC-MS, LC-MS/MS, nano-LC/ESI-MS/MS), ELISA, and synchrotron-based micro-analyses) in parallel to conservation intervention. Studies on samples from these cultural heritage objects have shown that each is composed of a polychromatic multilayered structure with sizing layers, ground layers, painted layers, and glaze. The carefully produced complex multilayered structures were examined using optical microscopy (visible and UV light) as well as synchrotron-based infrared microscopy, both of which revealed various organic and inorganic components in each layer. High sensitivity bulk MS and ELISA methods were used to further identify details regarding organic materials, such as fatty acids and collagens, and these results suggest different vegetable oils and animal species of glues. For example, cow milk casein and cow skin glue were identified in the Eastern Giant Buddha, suggesting that casein was used as a sizing agent and the cow skin glue as a binder for painting. The wall paintings from Cave N(a) (mid-7th century AD) were found to have horse glue used as sizing and drying oil (poppyseed/walnuts/perilla oils) as a binding media. The paintings’ complex structures and their organic and inorganic materials were fully understood using both imaging and bulk methods, and thus, these methods help to reconstruct historical wall painting techniques in full.

Background: Primary Sjögren’s syndrome (pSS) is a chronic inflammatory autoimmune disease characterized by lymphocyte infiltration in salivary and lacrimal glands. pSS affects primarily middle-aged and elderly patients, although younger age groups may also be involved. However, differences of etiology and pathogenesis between early-onset pSS (EOpSS) and late-onset pSS (LOpSS) are unknown. Recently, standardized outcome tools for measuring disease-specific activity and patients’ reported symptoms have been formulated by the European League Against Rheumatism (EULAR) SS study group: the EULAR SS Disease Activity Index (ESSDAI) for systemic features of pSS [1]. Also, as the new imaging techniques, salivary gland ultrasonography (SGUS) proved valuable for assessing salivary gland involvement in SS and seemed to exhibit good diagnostic properties. In addition, previous studies have demonstrated usefulness of SGUS for the prognostic stratification of patients with pSS [2], [3], [4]. Objectives: The aim of this study was to examine the differences of etiology and pathogenesis between EOpSS and LOpSS using ESSDAI and SGUS. Methods: Fifty-six pSS patients who fulfilled the American College of Rheumatology (ACR) / European League Against Rheumatism (EULAR) classification criteria for SS were studied. Based on the disease onset age, all pSS patients were divided into two groups as those with the onset age of 40 years old or younger (EOpSS: n=26) and those with the onset age of older than 65 years old (LOpSS: n=30). The clinical findings were evaluated ESSDAI and OMERACT SGUS score at the first visit to our hospital. The ESSDAI (0–123) proposes the evaluation of 12 domains or organ systems (constitutional, lymphadenopathy, glandular, articular, cutaneous, pulmonary, renal, peripheral nervous system, central nervous system, muscular, hematological and biology). All patients were examined SGUS by a single investigator who was blinded to device (TUS-A300; Canon Medical Systems, Tokyo, Japan) with a linear transducer (7.5-10MHz). The OMERACT SGUS score was used for graded changes in the parenchymal homogeneity of salivary glands: grade 0, normal-appearing salivary gland parenchyma; grade 1, minimal change: mild inhomogeneity without hypo/anechoic areas; grade 2, moderate change: moderate inhomogeneity with focal hypo/anechoic areas; grade 3, severe change: diffuse inhomogeneity with hypo/anechoic areas occupying the entire gland surface [5]. Results: The proportions of positive sera of RF, anti-SS-A and anti-SS-B antibodies were not different in the two groups, but the disease activities were higher in the EOpSS than in the LOpSS patients by measuring ESSDAI (7.30 vs 4.23, p=0.008), especially in constitutional domain (1.50 vs 0.60, p=0.03), articular domain (1.54 vs 0.40, p=0.0002) and biological domain (1.35 vs 0.90, p=0.04). No difference in salivary secretion was found between two groups (EOpSS: 8.02 vs LOpSS: 6.31 mL/10min.), but the OMERACT SGUS score was higher in LOpSS than in EOpSS patients (2.00 vs 2.70, p=0.0002). Conclusion: Although serological findings were not different, EOpSS patients had higher disease activity but less severe salivary gland degeneration than that in LOpSS patients, suggesting the pathogenesis of these two groups was different. References: [1]Seror R, et al. Ann Rheum Dis. 2010 Jun;69(6):1103-9. [2]Arthritis Care Res (Hoboken). 2014 Jul;66(7):1102-7. [3]Hammenfors DS, et al. Clin Exp Rheumatol. 2015 Jan-Feb;33(1):56-62. [4]Milic V, et al. PLoS One. 2019 Dec 31;14(12): e0226498. [5]Jousse-Joulin S, et al. Ann Rheum Dis. 2019 Jul;78(7):967-973. Disclosure of Interests: None declared

We oxidized histidine residues in monoclonal antibody drugs of immunoglobulin gamma 1 (IgG1) using ultraviolet C irradiation (UVC: 200–280 nm), which is known to be potent for sterilization or disinfection. Among the reaction products, we identified asparagine and aspartic acid by mass spectrometry. In the photo-induced oxidation of histidine in angiotensin II, ¹⁸O atoms from H₂¹⁸O in the solvent were incorporated only into aspartic acid but not into asparagine. This suggests that UVC irradiation generates singlet oxygen and induces [2 + 2] cycloaddition to form a dioxetane involving the imidazole C^γ − C^δ2 bond of histidine, followed by ring-opening in the manner of further photo-induced retro [2 + 2] cycloaddition. This yields an equilibrium mixture of two keto-imines, which can be the precursors to aspartic acid and asparagine. The photo-oxidation appears to occur preferentially for histidine residues with lower pK_a values in IgG1. We thus conclude that the damage due to UVC photo-oxidation of histidine residues can be avoided in acidic conditions where the imidazole ring is protonated.

Pyridoxal 5′-phosphate (PLP)-enzymes are essentially involved in amino acid and amine metabolism of a wide variety of organisms. Despite their extensive biochemical studies, there are little evidence and structural data to comprehensively elaborate the catalytic mechanism. We obtained X-ray snapshots of l-methionine γ-lyase from Entamoeba histolytica (EhMGL), a PLP-enzyme catalyzing the γ-elimination reaction of methionine. Here, we suggest a catalytic mechanism of EhMGL by using the X-ray snapshots covering all stages of this multistep catalysis reaction. Initial formation of a Michaelis complex is followed by the migration of double bond from the C4′=Nα–Cα moiety in an intermediate PLP-methionine imine to C4′–Nα=Cα in pyridoxamine 5′-phosphate (PMP)-α,β-dehydromethionine imine without intervention of a putative quinonoid intermediate. The enzyme can facilitate the subsequent γ-elimination of methanethiol by the possible general acid-base catalysis of Tyr108 for the E1cB mechanism, enabling to form the ene-imine C4′–Nα=Cα–Cβ=Cγ structure with the s-cis conformation, which is prerequisite for the non-enzymatic symmetry-allowed suprafacial [1,5]-hydrogen shift to complete the catalytic cycle by releasing α-ketobutyrate. The mechanism based on the X-ray snapshots is consistent with the reactivity of MGL toward methionine analogues. The generality of such a mechanism involving non-enzymatic concerted reaction in other PLP enzymes is discussed.

We present a mass spectrometric method for analyzing protein structure and function, based on the imidazole C-2 or histidine C^ε1 hydrogen/deuterium (H/D) exchange reaction, which is intrinsically second-order with respect to the concentrations of the imidazolium cation and OD^– in D₂O. The second-order rate constant (k₂) of this reaction was calculated from the pH dependency of the pseudo-first-order rate constant (k_φ) obtained from the change in average mass [ΔM_r (0 ≤ ΔM_r < 1)] of a peptide fragment containing a defined histidine residue at incubation time (t) such that k_φ = −[ln(1 – ΔM_r)]/t. We preferred using k₂ rather than k_φ because k₂^max (maximal value of k₂) was empirically related to pK_a as illustrated with a Brønsted plot [log k₂^max = −0.7pK_a + α (α is an arbitrary constant)], so that we could analyze the effect of structure on the H/D exchange rate in terms of log(k₂^max/k₂) representing the deviation of k₂ from k₂^max. In the catalytic site of bovine ribonuclease A, His12 showed a change in log(k₂^max/k₂) much larger than that of His119 upon binding with cytidine 3′-monophosphate, as anticipated from the X-ray structures and the possible change in solvent accessibility. However, we need to consider the hydrogen bonds of the imidazole group with nondissociable groups to interpret an extremely slow H/D exchange rate of His48 in a partially solvent-exposed situation.

We present here an approach to C-terminal sequencing of proteins by the procedure consisting of the following: (1) derivatization of the C-terminal α-carboxyl group with 3-aminopropyltris(2,4,6-trimethoxyphenyl)-phosphonium bromide (TMPP-propylamine) through oxazolone chemistry, (2) enzymatic proteolysis of the TMPP-derivatized protein, and (3) MALDI-MS/MS analysis of the peptide mixture, in which the C-terminal peptide incorporating the TMPP group is preferably detected. In this protocol, it is possible to choose any endoproteinase such as trypsin, GluC, and AspN for digestion so that a C-terminal peptide with length appropriate for mass spectrometric sequencing could be generated. The peptide labeled with TMPP-propylamine at the C terminus tends to exhibit y-type ions in MS/MS spectra, allowing manual sequence interpretation with the simplified fragmentation pattern. The efficacy of the method was verified with five proteins, which demonstrated that the C-terminal peptides were readily distinguishable by their peak intensity and characteristic mass signature peak in MALDI-PSD analysis.