Deuterium Labeling of Isoaspartic and Isoglutamic Acids for Mass Spectrometry Analysis.

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 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.

A New Chemotactic Mechanism Governs Long-Range Angiogenesis Induced by Patching an Arterial Graft into a Vein.

Chemotaxis, the migration of cells in response to chemical stimulus, is an important concept in the angiogenesis model. In most angiogenesis models, chemotaxis is defined as the migration of a sprout tip in response to the upgradient of the VEGF (vascular endothelial growth factor). However, we found that angiogenesis induced by performing arterial patch grafting on rabbits occurred under the decreasing VEGFA gradient. Data show that the VEGFA concentration peaked at approximately 0.3 to 0.5 cm away from the arterial patch and decreased as the measurement approaches the patch. We also observed that the new blood vessels formed are twisted and congested in some areas, in a distinguishable manner from non-pathological blood vessels. To explain these observations, we developed a mathematical model and compared the results from numerical simulations with the experimental data. We introduced a new chemotactic velocity using the temporal change in the chemoattractant gradient to govern the sprout tip migration. We performed a hybrid simulation to illustrate the growth of new vessels. Results indicated the speed of growth of new vessels oscillated before reaching the periphery of the arterial patch. Crowded and congested blood vessel formation was observed during numerical simulations. Thus, our numerical simulation results agreed with the experimental data.

Genetic and clinical prediction models for the efficacy and hepatotoxicity of methotrexate in patients with rheumatoid arthritis: a multicenter cohort study.

The objective of the study is to develop genetic and clinical prediction models for the efficacy and hepatotoxicity of methotrexate (MTX) in patients with rheumatoid arthritis (RA). Among RA patients treated with MTX, 1966 polymorphisms of 246 enzymes/transporters relevant to pharmacokinetics and pharmacodynamics were measured by the Drug Metabolism Enzymes and Transporters (DMET) microarray and direct sequencing, and clinical variables at baseline were collected. For efficacy, response criteria of the European League Against Rheumatism were used to classify patients as responders or non-responders. Hepatotoxicity was defined as elevations of aspartate aminotransferase or alanine aminotransferase ≥1.5 times the reference range upper limit. Among 166 patients, a genetic prediction model for efficacy using seven polymorphisms showed the area under the receiver operating characteristic curve (AUC) was 0.822, with 74.3% sensitivity and 76.8% specificity. A combined genetic and clinical model indicated the AUC was 0.844, with 81.5% sensitivity and 76.9% specificity. By incorporating clinical variables into the genetic model, the overall category-free net reclassification improvement (NRI) was 0.663 (P < 0.0001) and the overall integrated discrimination improvement (IDI) was 0.083 (P = 0.0009). For hepatotoxicity, a genetic prediction model using seven polymorphisms showed the AUC was 0.783 with 70.0% sensitivity and 80.0% specificity, while the combined model indicated the AUC was 0.906 with 85.1% sensitivity and 87.8% specificity (overall category-free NRI: 1.002, P < 0.0001; overall IDI: 0.254, P < 0.0001). Our genetic and clinical models demonstrated moderate diagnostic accuracy for MTX efficacy and high accuracy for hepatotoxicity. These findings should, however, be validated and interpreted with a caution until external validation.

Multi-Modal Compositional Analysis of Layered Paint Chips of Automobiles by the Combined Application of ATR-FTIR Imaging, Raman Microspectrometry, and SEM/EDX.

For the forensic analysis of multi-layered paint chips of hit-and-run cars, detailed compositional analysis, including minor/trace chemical components in the multi-layered paint chips, is crucial for the potential credentials of the run-away car as the number of layers, painting process, and used paints are quite specific to the types of cars, color of cars, and their surface protection depending on the car manufacturer and the year of manufacture, and yet overall characteristics of some paints used by car manufacturers might be quite similar. In the present study, attenuated total reflectance-Fourier transform infrared (ATR-FTIR) imaging, Raman microspectrometry (RMS), and scanning electron microscopy/energy-dispersive X-ray spectrometric (SEM/EDX) techniques were performed in combination for the detailed characterization of three car paint chip samples, which provided complementary and comprehensive information on the multi-layered paint chips. That is, optical microscopy, SEM, and ATR-FTIR imaging techniques provided information on the number of layers, physical heterogeneity of the layers, and layer thicknesses; EDX on the elemental chemical profiles and compositions; ATR-FTIR imaging on the molecular species of polymer resins, such as alkyd, alkyd-melamine, acrylic, epoxy, and butadiene resins, and some inorganics; and RMS on the molecular species of inorganic pigments (TiO2, ZnO, Fe3O4), mineral fillers (kaolinite, talc, pyrophyllite), and inorganic fillers (BaSO4, Al2(SO4)3, Zn3(PO4)2, CaCO3). This study demonstrates that the new multi-modal approach has powerful potential to elucidate chemical and physical characteristics of multi-layered car paint chips, which could be useful for determining the potential credentials of run-away cars.

Multicomponent Coupling Reaction Using Arynes: Synthesis of Xanthene Derivatives.

One-pot synthesis of xanthene derivatives was achieved by a route involving the cascade three-component coupling reaction of arynes with DMF and active methylenes followed by the SN2' reaction of three-component coupling products with thiols. The reactivity of three-component coupling products toward nucleophiles and the further conversion of oxygen heterocycles allowing facile incorporation of structural variety were studied.

Significance of Histidine Hydrogen-Deuterium Exchange Mass Spectrometry in Protein Structural Biology.

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.

Mycophenolate mofetil versus intravenous cyclophosphamide for induction treatment of proliferative lupus nephritis in a Japanese population: a retrospective study.

OBJECTIVES: Recent studies have shown that mycophenolate mofetil (MMF) is similar to intravenous cyclophosphamide (IVC) for the treatment of lupus nephritis (LN), but that treatment response may vary according to location and race/ethnicity. Moreover, no studies have been conducted to compare the efficacy of MMF with that of IVC for a Japanese population. We therefore conducted a retrospective study to clarify the efficacy and safety of MMF compared with that of IVC for induction therapy for active LN, classes III and IV, in a Japanese population of 21 patients, 11 of whom received MMF and 10 IVC. METHODS: The primary endpoint was expressed as the percentage of responders, who in turn were defined as the patients who met complete or partial response criteria according to the European consensus statement. The secondary endpoints comprised the renal activity component and serological activity. RESULTS: The primary endpoint was achieved in nine (81.8 %) patients receiving MMF and in four (40.0 %) receiving IVC, with no significant difference between the two groups (p = 0.081), while there was also no significant difference between them in terms of secondary endpoints. However, the MMF group suffered significantly fewer hematologic toxic effects than the IVC group. CONCLUSIONS: MMF may be used as an alternative to IVC for inducing renal remission of LN in Japanese patients.

C-terminal sequencing of protein by MALDI mass spectrometry through the specific derivatization of the α-carboxyl group with 3-aminopropyltris-(2,4,6-trimethoxyphenyl)phosphonium bromide.

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.

Similarities between Disaster Food and Space Food.

Disaster and space environments are similar in that they are closed environment, with limited lifelines. Here, we examined the similarity between disaster food and space food, to explore interactive problem-solving of food support for disaster and space environments. The Japan Disaster Food Certification Standards (Japan Disaster Food Society) and the Japanese Space Food Certification Standards (Japan Aerospace Exploration Agency) requirements and certified products, which were posted on the websites as of June 16, 2021, were compared. Certified products were classified into "staple foods," "main and/or side dishes," "milk and dairy products," "fruits," "confectionery and favorite beverages," "condiments," "dietary supplements," and "sets." Certification standards involved six items for Japan Disaster Food and eight items for Japanese Space Food. Most standards were similar. Concretely, both standards demanded room temperature storage, tough packaging and hygiene management in facilities. Both emphasized habitual food and easy eating. However, the best-by date was ≥6 mo for Japan Disaster Food, but ≥1.5 y for Japanese Space Food. In addition, Japanese Space Food required noted nutritious, food hygienic, eatable in space, cookable by specific equipment, endurable pressure by launch, and domestically produced food. There were 171 and 47 products of Japan Disaster Food and Japanese Space Food, respectively. Staple foods (pregelatinized rice, etc.) and main and/or side dishes were commonest among Japan Disaster Foods and Japanese Space Foods, respectively. It is possible to utilize of Space Food as Disaster Food, but there are some issues that must be cleared before "utilization of Disaster Food as Space Food."

Specific racemization of heavy-chain cysteine-220 in the hinge region of immunoglobulin gamma 1 as a possible cause of degradation during storage.

Therapeutic antibodies often suffer from degradation due to various modifications during storage. We detected a degradation of immunoglobulin gamma 1 (IgG1) stored for 6 month at 40 °C, and identified the modification as the racemization of Cys220 in the hinge sequence S(219)CDKTHT(225) of the heavy chain by tryptic peptide mapping and tandem mass spectrometry. The rate of racemization at Cys220 was enhanced deliberately by incubating the protein at 50 °C and pH 9.0, while all the other cysteine residues were not affected. The racemization of Cys220 was confirmed by mass spectrometry in conjunction with extracted ion chromatography of the tryptic digest of IgG1 forced to degrade in D(2)O and a series of synthetic hinge fragments containing D-amino acid, as well as the detection of D-cysteine in the acid hydrolysate. To rationalize the possible relationship between the racemization of Cys220 and isopeptide formation at the neighboring residue of Asp221, we suggest a new reaction mechanism that assumes a base catalyst to initiate these reactions by activating the amide nitrogen of Lys222. Due to the highly flexible nature of the hinge region, Lys222 can participate in either the formation of a cyclic imidazoline intermediate involving the α-carbonyl carbon of Cys220 to facilitate the racemization of Cys220 or that of a succinimide structure leading to the isomerization of Asp221.

A method for N-terminal de novo sequencing of Nα-blocked proteins by mass spectrometry.

A method for de novo sequencing of N(α)-blocked proteins by mass spectrometry (MS) is presented. The approach consists of enzymatic digestion of N(α)-blocked protein, recovery of N-terminal peptide by depletion of non-N-terminal peptides from the digest pool, and selective derivatization of a C-terminal α-carboxyl group of isolated N-terminal peptide. The C-terminal α-carboxyl group of the N-terminal peptide was selectively derivatized with 3-aminopropyl-tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP-propylamine), according to oxazolone chemistry. The reagent TMPP-propylamine was designed to facilitate sequence analysis with MALDI-MS by mass- and charge-tagging. All of the identities and N-terminal sequences of two N(α)-acetylated proteins (rabbit phosphorylase b and bovine calmodulin) and human orexin A, which has pyroglutamic acid at the N-terminus, were successfully analyzed by allowing for the y-type ions almost exclusively.

Role of imaging studies in the diagnosis and evaluation of giant cell arteritis in Japanese: report of eight cases.

The objective of this study is to clarify the characteristics and imaging results of Japanese patients with giant cell arteritis (GCA). Eight patients with biopsy-proven GCA were enrolled. Their clinical data and imaging results were retrospectively examined from their medical records. All the patients met the criteria for the classification of GCA by the American College of Rheumatology. Although the clinical manifestations are similar to those previously reported, none of the eight patients presented ocular symptoms, and half of them presented jaw claudication. Ultrasonography (US) of temporal artery showed the halo sign in all the patients. Fluorodeoxyglucose positron emission tomography (FDG-PET) was performed in four patients and indicated the presence of aortitis of the patients. US is a quick and noninvasive test to detect inflammation of temporal artery, and FDG-PET is very helpful for early diagnosis of aortitis in GCA. Awareness of the disease and appropriate imaging tests will result in diagnosis of GCA.

Hydrodynamic Approach for Revealing Venous Anastomotic Stenosis Formation Within a Dialysis Arteriovenous Graft.

A conventional arteriovenous graft in patients on dialysis often leads to anastomotic stenosis, which decreases the blood flow rate and increases the risk of complications. In this study, based on hydrodynamics, the pulsatile pressure at the blood vessel graft-vein junction was investigated experimentally and numerically for revealing the causes of stenosis formation and inward remodeling. In the experiments, the pulsatile pressure and displacement at the anastomotic connection were measured at a branched collapsible tube. It was revealed that the pressure becomes negative between pressure peaks of the pulsatile flow; furthermore, tube diameter changes in accordance with the pressure pulsation. Subsequently, numerical simulations revealed that a relatively large pressure difference occurs at the anastomotic connection because of flow collision and separation as compared with the other part, and the pulsatile pressure. Therefore, it is possible that vein at an anastomotic connection may change its shape under pulsating flow. Furthermore, it was found that the pressure difference slightly increased with the anastomosis angle, but the anastomosis angle did not affect the flow rate. Clinical trials in the next step are required to reveal the causal relationship between stenosis and the pulsatile pressure, but the pulsatile flow and its pressure are likely to be one factor in stenosis and inward remodeling.

Effect of UVC Irradiation on the Oxidation of Histidine in Monoclonal Antibodies.

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 Cγ - Cδ2 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 pKa 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.

A new approach for detecting C-terminal amidation of proteins and peptides by mass spectrometry in conjunction with chemical derivatization.

We describe a mass spectrometric method for distinguishing between free and modified forms of the C-terminal carboxyl group of peptides and proteins, in combination with chemical approaches for the isolation of C-terminal peptides and site-specific derivatization of the C-terminal carboxyl group. This method could most advantageously be exploited to discriminate between peptides having C-terminal carboxyl groups in the free (COOH) and amide (CONH(2)) forms by increasing their mass difference from 1 to 14 Da by selectively converting the free carboxyl group into methylamide (CONHCH(3)). This method has been proven to be applicable to peptides containing aspartic and glutamic acids, because all the carboxyl groups except the C-terminal one are inert to derivatization, according to oxazolone chemistry. The efficiency of the method is illustrated by a comparison of the peaks of processed peptides obtained from a mixture of adrenomedullin, calcitonin, and BSA. Among these components of the mixture, only the C-terminal peptide of BSA exhibited the mass shift of 13 Da upon treatment, eventually unambiguously validating the C-terminal amide structures of adrenomedullin and calcitonin. The possibility of extending this method for the analysis of C-terminal PTMs is also discussed.

Terminal proteomics: N- and C-terminal analyses for high-fidelity identification of proteins using MS.

In proteomics, MS plays an essential role in identifying and quantifying proteins. To characterize mature target proteins from living cells, candidate proteins are often analyzed with PMF and MS/MS ion search methods in combination with computational search routines based on bioinformatics. In contrast to shotgun proteomics, which is widely used to identify proteins, proteomics based on the analysis of N- and C-terminal amino acid sequences (terminal proteomics) should render higher fidelity results because of the high information content of terminal sequence and potentially high throughput of the method not requiring very high sequence coverage to be achieved by extensive sequencing. In line with this expectation, we review recent advances in methods for N- and C-terminal amino acid sequencing of proteins. This review focuses mainly on the methods of N- and C-terminal analyses based on MALDI-TOF MS for its easy accessibility, with several complementary approaches using LC/MS/MS. We also describe problems associated with MS and possible remedies, including chemical and enzymatic procedures to enhance the fidelity of these methods.

Determination of pKa values of individual histidine residues in proteins using mass spectrometry.

We developed a mass spectrometric method to determine the p K a values of individual histidine residues in proteins. The method is based on the fact that the imidazole C 2-proton undergoes pH-dependent hydrogen-deuterium exchange reaction, of which the rate constant ( k phi) reflects the p K a for the ionization of imidazole to imidazolium. The experimental procedure consists of the following: (1) protein incubation in D 2O solvent at various pH values, (2) protein digestion by proteolytic enzyme(s), during which all the rapidly exchanging deuterons such as those in amide and hydroxyl groups are back-exchanged for protons, and (3) measurement of the mass spectrum of each histidine-containing peptide by LC/ESI-MS. The k phi of the H-D exchange reaction is obtained from the mass spectrum reflecting the extent of deuterium incorporation. The p K a value is then determined from a plot of k phi versus pH, which gives a typical sigmoidal curve. Unambiguous assignment of the p K a values to individual histidine residues can be achieved simultaneously based on the observed molecular mass of the peptide. The p K a values of three of four histidine residues (His12, -105, and -119) in RNase A were successfully determined by this method and were in good agreement with those determined by (1)H NMR and hydrogen-tritium exchange methods. The method uses subnanomole quantities of protein, allowing measurement at a much lower concentration than that of 1 mM required for the conventional NMR approach that is currently almost exclusively the method of choice.

Meta-analysis: diagnostic accuracy of anti-cyclic citrullinated peptide antibody and rheumatoid factor for rheumatoid arthritis.

BACKGROUND: Rheumatoid factor (RF) and autoantibodies against cyclic citrullinated peptide (CCP) are markers that might help physicians diagnose rheumatoid arthritis. PURPOSE: To determine whether anti-CCP antibody more accurately identifies patients with rheumatoid arthritis and better predicts radiographic progression than does RF. DATA SOURCES: MEDLINE through September 2006 and reference lists of retrieved studies and review articles. STUDY SELECTION: Studies in any language that enrolled at least 10 participants and that examined the role of anti-CCP antibody and RF in the diagnosis or prognosis of known or suspected rheumatoid arthritis. DATA EXTRACTION: Two authors independently evaluated studies for inclusion, rated methodological quality, and abstracted relevant data. DATA SYNTHESIS: The DerSimonian-Laird random-effects method was used to summarize sensitivities, specificities, and positive and negative likelihood ratios from 37 studies of anti-CCP antibody and 50 studies of RF. The pooled sensitivity, specificity, and positive and negative likelihood ratios for anti-CCP antibody were 67% (95% CI, 62% to 72%), 95% (CI, 94% to 97%), 12.46 (CI, 9.72 to 15.98), and 0.36 (CI, 0.31 to 0.42), respectively. For IgM RF, the values were 69% (CI, 65% to 73%), 85% (CI, 82% to 88%), 4.86 (CI, 3.95 to 5.97), and 0.38 (CI, 0.33 to 0.44). Likelihood ratios among IgM RF, IgG RF, and IgA RF seemed to be similar. Results from studies of patients with early rheumatoid arthritis were similar to those from all studies. Three of 4 studies found that risk for radiographic progression was greater with anti-CCP antibody positivity than with IgM RF positivity. LIMITATIONS: Many studies had methodological limitations. Studies of RF were heterogeneous and had wide ranges of sensitivity and specificity. CONCLUSIONS: Anti-CCP antibodies are more specific than RF for diagnosing rheumatoid arthritis and may better predict erosivedisease.