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PubMed1995

Effects of dietary modification and fish oil supplementation on dyslipoproteinemia in pediatric systemic lupus erythematosus.

OBJECTIVE: To determine if a program of dietary modification and fish oil supplementation is effective in treating the dyslipoproteinemia in pediatric systemic lupus erythematosus (SLE). METHODS: Prospective clinical trial where each patient serves as his/her own control. Twenty-four consecutive adolescents fulfilling SLE classification criteria were screened with fasting lipid profiles. Patients were identified as having dyslipoproteinemia of active disease or of corticosteroid therapy. Patients were treated for 6 weeks with dietary modification and if dyslipoproteinemia did not normalize with another 6 weeks of dietary modification and fish oil supplementation. RESULTS: Seventeen patients (71%) had dyslipoproteinemia; 10 of active disease, 4 of steroid therapy; 3 with a combined pattern. Eleven patients underwent dietary modification. There was a significant decrease in serum triglyceride concentrations (p < 0.05). Total cholesterol, low density lipoprotein cholesterol, and high density lipoprotein cholesterol did not change significantly. A further significant decline in serum triglycerides was achieved with fish oil supplementation (p < 0.05). Five of the 11 patients who underwent treatment continued to have dyslipoproteinemia. CONCLUSION: Dyslipoproteinemia is common in pediatric SLE. Dietary modification and fish oil supplementation appear to be effective in improving serum lipid profiles, and blinded studies are warranted. a significant number of patients may require pharmacologic therapy for persistent dyslipoproteinemia to prevent complications of premature atherosclerosis.

Adolescent↗
PubMed1994

Lipid modification of bacterial prolipoprotein. Transfer of diacylglyceryl moiety from phosphatidylglycerol.

The peptide, MKATKLVLGAVILGSTLLAGCSSN, corresponding to the N-terminal 24 amino acids of Braun's prolipoprotein, was used to study the lipid modification of prolipoprotein in Escherichia coli by measuring the rate of incorporation of either [2-3H]glycerol or [9,10-3H]palmitate from the corresponding labeled phosphatidylglycerol into the peptide. Using E. coli strains containing varying levels of prolipoprotein diacylglyceryl modification activities due to mutations in or overexpression of the gene involved in diacylglyceryl modification (lgt), we have shown that the activities based on the peptide assay correlated well with the prolipoprotein-based assay. Further, we have followed the fate of the lipid substrate, phosphatidylglycerol, during the modification reaction and found that lipid modification of prolipoprotein involves the transfer of diacylglyceryl moiety from phosphatidylglycerol to the sulfhydryl group of the cysteine residue with the concomitant formation of sn-glycerol 1-phosphate. This mechanism is contrary to the previously proposed two-step mechanism of an initial glyceryl transferase followed by O-acyl transfer (Chattopadhyay, P.K., and Wu, H.C. (1977) Proc. Natl. Acad. Sci. U. S. A. 74, 5318-5322). Accordingly, the enzyme that catalyzes this activity has been named phosphatidylglycerol-prolipoprotein diacylglyceryl transferase. The revised pathway for the lipoprotein biogenesis in bacteria consists of three successive reactions catalyzed by prolipoprotein diacylglyceryl transferase, signal peptidase II, and apolipoprotein N-acyltransferase.

Amino Acid Sequence↗
PubMed1978

[Modifications of lymphocyte HL-A antigens as a consequence of therapy in patients with manic-depressive psychosis].

In 54 (= 46.96%) of 115 patients with maniacal-depressive psychosis a HLA modification could be identified. This modification turned out to be temporary and from a serological point of view it revealed a different character. In 29 cases a loss of HLA antigens could be observed, in 3 cases there was a decrease, in 14 cases a combination of both changes, twice a polyreactivity was observed and 6 times a change of the antigen HLA-A 2 in A 28 could be determined. These serological modifications appeared after therapy with lithium as well as with various antidepressive and neuroleptic medicaments. The connection between therapy and development of HLA modification could be ensured statistically. The modifications of HLA antigens A 10 and B 7 developed after administering neuroleptic medicaments, those of HLA antigens A 9, A 11, B 12, and B 13 after therapy with antidepressive medicaments. HLA antigens B 27 and B 40 showed a relative resistance towards therapy. The significance of these findings for the possibility of mistakes in HLA typing and from the standpoint of therapy efficiency in connection with the patient's HLA phaenotype is discussed.

Antipsychotic Agents↗
PubMed1996

Mutagenic DNA base modifications are correlated with lesions in nonneoplastic hepatic tissue of the English sole carcinogenesis model.

Hydroxyl radical-induced mutagenic base modifications have been linked to neoplasia in a number of biological systems, including English sole from chemically contaminated urban environments. However, virtually no information exists on the relationship between the mutagenic base modifications and preneoplastic and other lesions found in tumor-free tissues prone to cancer. We studied six hepatic lesions in immature, neoplasm-free English sole exposed to an urban and reference environment and established correlations between the lesion incidence and concentrations of the mutagenic base modifications 8-hydroxyguanine and 8-hydroxyadenine. The lesions were putatively preneoplastic basophilic foci, hepatocellular karyomegaly, megalocytic hepatosis, hepatocellular vacuolar change, hyalin droplet formation, and apoptosis. With the exception of hepatocellular vacuolar change, significant positive correlations were found between the lesions and the mutagenic base modifications. The hydroxyl radical may be a common etiological factor in the formation of the base modifications and hepatic lesions.

Adenine↗
PubMed1997

Oxidative and malondialdehyde modification of low-density lipoprotein: a comparative study.

Low-density lipoprotein (LDL) was modified with copper ions (Cu2+) and malondialdehyde (MDA), and the differences were compared. The results show that both oxidative and MDA modification produce a decrease in free amino groups in LDL and enhance its electrophoretic mobility on agarose gel, and that these observations are linked. However, differences produced by the two forms of modification were observed. Oxidative modification of LDL involves free radical-mediated lipid peroxidation which produces large amounts of thiobarbituric acid-reactive substances (TBARS) and conjugated dienes. In addition, vitamin E was reduced considerably and cholesterol lowered, and apolipoprotein B (apo B) fragmentation and aggregation were seen. Similar changes were not seen with MDA modification which does not involve lipid peroxidation. Fluorescence emission spectra of both forms of modified LDL show that emission intensity increases gradually as the modification progresses, but maximum emission wavelength and spectrum patterns are not the same. These findings may be of some significance in the study of the antigenicity, scavenger receptor multiplicity and toxic effects of modified LDL.

Copper↗
PubMed1998

[Improvement of intestinal absorption of peptide and protein drugs by chemical modification with fatty acids].

It is well known that the oral bioavailability of peptide and protein drugs is generally poor because they are extensively degraded by proteases in the gastrointestinal tract and impermeable through the intestinal mucosa. Therefore, various approaches have been examined to overcome the delivery problems of these peptides and to improve their absorption via the gastrointestinal tract. Of these approaches, a potentially useful approach to solve these delivery problems may be chemical modification of peptides and proteins to produce prodrugs and analogues. Thus, it is plausible that this approach may protect peptides against degradation by peptidases and other enzymes present at the mucosal barrier and renders the peptides and proteins more lipophilic, resulting in increased bioavailability. From these standpoints, we synthesized lipophilic derivatives of peptides and proteins such as thyrotropin-releasing hormone (TRH), tetragastrin (TG), calcitonin and insulin by chemical modification with fatty acids. The pharmacological activities of these derivatives were relatively high as compared with the native peptides. A significant increase in the intestinal absorption of these derivatives of peptides was observed in comparison with native peptides. Overall, the effects of acylation on the intestinal absorption of these peptides were more predominant in the large intestine than those in the small intestine. In addition, these derivatives were more stable than the parent peptides in homogenates of the various intestinal mucosae. We also examined the intestinal transport characteristics of TG and its acyl derivatives using Caco-2 cell monolayers in order to assess the contribution of enzymatic and transport barriers on their intestinal absorption. The degradation clearance of TG on the apical membrane was decreased by chemical modification with fatty acids. In addition, the permeability clearance of TG was improved by the acylation. On the other hand, the intestinal absorption of thyrotropin releasing hormone (TRH), which is transported by a carrier-mediated process, was also enhanced by chemical modification with lauric acid. In summary, this chemical modification approach may be useful to improve the intestinal absorption of peptide and protein drugs.

Acylation↗
PubMed1997

Effect of chemical modification of oligohomopyrimidine on triplex formation: thermodynamic and kinetic studies.

To investigate the effect of chemical modification of the third strand on the stability of triplex DNA, we have examined the thermodynamic properties of the triplex formation between a 23-mer double-stranded homopurine-homopyrimidine and each of five kinds of 15-mer chemically modified single-stranded homopyrimidines by isothermal titration calorimetry, and the kinetic properties by interaction analysis system. The modifications of the third strand included two base modifications, two sugar moiety modifications, and one phosphate backbone modification. The thermodynamic and kinetic parameters for the triplex formation were similar in magnitude among the two base-modified and two sugar-modified single strands. By contrast, the binding constant for the triplex formation with the single strand with phosphorothioate backbone was more than ten times as small as that for the other triplex formation. On the basis of the kinetic analyses, the single strand with phosphorothioate backbone was more difficult to associate with and easier to dissociate from the target double strand than the other single strands, which resulted in the much smaller binding constant.

Base Sequence↗
PubMed1998

Affinity modification of phenylalanyl-tRNA synthetase from Thermus thermophilus by tRNAPhe transcripts containing 4-thiouridine.

Photoreactive derivatives of tRNAPhe containing residues of 4-thiouridine (s4U) were synthesized by the transcription system of T7 RNA polymerase. Complete substitution of s4U for 16 uridine residues ([16s4U]-tRNAPhe) caused a 14-fold decrease in the catalytic efficiency of aminoacylation of the tRNAPhe transcript by phenylalanyl-tRNA synthetase from T. thermophilus. [1s4U]-tRNAPhe obtained by random incorporation of s4U residues with further isolation of s4U-monosubstituted RNA molecules on an affinity gel has the same kinetic parameters in aminoacylation as the tRNAPhe transcript. The s4U-containing tRNAPhe transcripts were shown to bind covalently to phenylalanyl-tRNA synthetase, and the specificity of modification was demonstrated. The modification stoichiometry determined in this work suggests that the enzyme is a functional dimer. The modification labels both alpha- and beta-subunits of the enzyme, which has an oligomeric structure of alpha2beta2, and forms "cross-linking" products of subunits upon modification with [16s4U]-tRNAPhe. The prevalence of modification of the alpha-subunit suggests that tRNA has contacts with the enzyme, which have not been deciphered previously by X-ray analysis.

Base Sequence↗
PubMed1998

Methylglyoxal-derived modifications in lens aging and cataract formation.

PURPOSE: To determine whether the Maillard reaction of methylglyoxal is associated with human lens aging and cataractogenesis and to investigate how glutathione depletion affects methylglyoxal-derived modifications in organ-cultured lenses. METHODS: Antibodies against methylglyoxal-derived modifications were developed in rabbits and purified by immunoaffinity chromatography. A competitive enzyme-linked immunosorbent assay (ELISA) measured methylglyoxal-derived products in human lens proteins. Lenses of galactosemic rats grown in organ culture were used to assess the role of glutathione-dependent pathways in methylglyoxal metabolism and Maillard reactions. RESULTS: Methylglyoxal-derived modifications in the human lens were age dependent, and brunescent lenses had the highest levels of these modifications. Immunofluorescence staining identified antigens distributed throughout the lens, with higher levels in old lenses than in younger ones. Experiments with normal or galactosemic rat lenses grown in organ culture showed that lens proteins do not have an increase in methylglyoxal-modified proteins when cultured in medium containing 500 microM methylglyoxal alone, but they accumulate modified proteins when cultured with DL-glyceraldehyde. Inclusion of 30 mM glucose in the medium marginally increased methylglyoxal-derived products, but there was no correlation between lens glutathione content and methylglyoxal-derived modifications. CONCLUSIONS: Methylglyoxal-mediated Maillard reactions that occur in the human lens may play a role in lens aging and cataract formation. Methylglyoxal is probably derived from metabolic pathways within the lens. Decreased glutathione in organ-cultured rat lenses does not significantly influence methylglyoxal-mediated Maillard reactions.

Adolescent↗
PubMed2000

Diversity of restriction-modification gene homologues in Helicobacter pylori.

The complete genome sequences of two Helicobacter pylori strains have recently become available. We have searched them for homologues of restriction-modification genes. One strain (26695) carried 52 such homologues, and the other (J99) carried 53. Their sequence alignments were arranged in the form of a phylogenetic tree and compared with the tree based on rRNA. The trees showed that the homologues are scattered among diverse groups of bacteria. They also revealed high polymorphism within the species--there are 42 pairs with high homology, 10 specific to 26695, and 11 specific to J99. Many of the restriction-modification homologues were characterized by a GC content lower than that of the average gene in the genome. Some of the restriction-modification homologues showed a different codon use bias from the average genes. These observations are interpreted in terms of horizontal transfer of the restriction-modification genes.

Base Composition↗
PubMed2001

Characterization of AloI, a restriction-modification system of a new type.

We report the properties of the new AloI restriction and modification enzyme from Acinetobacter lwoffi Ks 4-8 that recognizes the DNA target 5' GGA(N)6GTTC3' (complementary strand 5' GAAC(N)6TCC3'), and the nucleotide sequence of the gene encoding this enzyme. AloI is a bifunctional large polypeptide (deduced M(r) 143 kDa) revealing both DNA endonuclease and methyltransferase activities. Depending on reaction cofactors, AloI cleaves double-stranded DNA on both strands, seven bases on the 5' side, and 12-13 bases on the 3' side of its recognition sequence, and modifies adenine residues in both DNA strands in the target sequence yielding N6-methyladenine. For cleavage activity AloI maintains an absolute requirement for Mg(2+) and does not depend on or is stimulated by either ATP or S-adenosyl-L-methionine. Modification function requires the presence of S-adenosyl-L-methionine and is stimulated by metal ions (Ca(2+)). The C-terminal and central parts of the protein were found to be homologous to certain specificity (HsdS) and modification (HsdM) subunits of type I R-M systems, respectively. The N-terminal part of the protein possesses the putative endonucleolytic motif DXnEXK of restriction endonucleases. The deduced amino acid sequence of AloI shares significant homology with polypeptides encoding HaeIV and CjeI restriction-modification proteins at the N-terminal and central, but not at the C-terminal domains. The organization of AloI implies that its evolution involved fusion of an endonuclease and the two subunits, HsdM and HsdS, of type I restriction enzymes. According to the structure and function properties AloI may be regarded as one more representative of a newly emerging group of HaeIV-like restriction endonucleases. Discovery of these enzymes opens new opportunities for constructing restriction endonucleases with a new specificity.

Acinetobacter↗
PubMed2026

Lysine methylation is an endogenous post-translational modifications of tau protein in human brain and a modulator of aggregation propensity.

Tau protein undergoes a broad range of post-translational modifications in the brain, influencing its structure, solubility, and propensity to aggregate. This chapter presents an integrated methodological framework for characterizing tau methylation and evaluating its impact on tau biology. We describe procedures for isolating soluble and filamentous tau from post-mortem human brain tissue while preserving modifications for proteomic analysis. These approaches support precise mapping of methylation sites alongside other co-occurring modifications. To model methylation under controlled conditions, we outline protocols for recombinant tau expression, purification, and chemical reductive methylation, including radiolabeled assays for determining modification stoichiometry. We then detail biophysical assays used to assess how methylation alters tau conformation and aggregation propensity. This methodological framework supports experimentation seeking insight into mechanisms relevant to Alzheimer's disease and related tauopathies.

Humans↗
PubMed2026

Post-translational chemical modification of E3 ligase for efficient target protein degradation.

Targeted protein degradation (TPD) has emerged as a powerful therapeutic strategy, with proteolysis-targeting chimeras (PROTACs) leading efforts to address previously undruggable targets. However, PROTACs face challenges such as low bioavailability and poor pharmacokinetic properties which limit their biological applications. Here, we report a strategy termed post-translational chemical modification targeting chimera (PTcM-TAC), which integrates ligand-directed chemistry into the PROTAC framework to achieve sustained target protein degradation through covalent modification of E3 ligases. PTcM-TAC incorporates an electrophilic dibromophenyl benzoate warhead into the linker connecting the E3 ligase ligand and the protein-of-interest (POI) ligand, enabling selective transfer of the POI ligand onto the recruited E3 ligase while releasing the E3-binding moiety. Mechanistic studies, including LC-MS/MS peptide mapping, pull-down assays, and structural modeling, demonstrated site-selective modification of CRBN by the PTcM-TAC. The resulting ligand-labeled E3 ligase enables sustained pseudo-catalytic target recognition through a simplified binary interaction, thereby maintaining degradation activity even after compound washout. Furthermore, we successfully applied the PTcM-TAC strategy to another representative E3 ligase, von Hippel-Lindau (VHL), which exhibited substantially sustained degradation activity compared with conventional PROTACs. To our knowledge, PTcM-TAC represents the first ligand-directed chemical strategy that converts transient PROTAC-mediated ternary complex formation into binary target recognition via post-translational chemical modification of an E3 ligase. We believe that PTcM-TAC could provide a platform for next-generation targeted protein degraders to overcome the current limitation of PROTAC approach.

Ubiquitin-Protein Ligases↗
PubMed2006

Plasmid-encoded antirestriction protein ArdA can discriminate between type I methyltransferase and complete restriction-modification system.

Many promiscuous plasmids encode the antirestriction proteins ArdA (alleviation of restriction of DNA) that specifically affect the restriction activity of heterooligomeric type I restriction-modification (R-M) systems in Escherichia coli cells. In addition, a lot of the putative ardA genes encoded by plasmids and bacterial chromosomes are found as a result of sequencing of complete genomic sequences, suggesting that ArdA proteins and type I R-M systems that seem to be widespread among bacteria may be involved in the regulation of gene transfer among bacterial genomes. Here, the mechanism of antirestriction action of ArdA encoded by IncI plasmid ColIb-P9 has been investigated in comparison with that of well-studied T7 phage-encoded antirestriction protein Ocr using the mutational analysis, retardation assay and His-tag affinity chromatography. Like Ocr, ArdA protein was shown to be able to efficiently interact with EcoKI R-M complex and affect its in vivo and in vitro restriction activity by preventing its interaction with specific DNA. However, unlike Ocr, ArdA protein has a low binding affinity to EcoKI Mtase and the additional C-terminal tail region (VF-motif) is needed for ArdA to efficiently interact with the type I R-M enzymes. It seems likely that this ArdA feature is a basis for its ability to discriminate between activities of EcoKI Mtase (modification) and complete R-M system (restriction) which may interact with unmodified DNA in the cells independently. These findings suggest that ArdA may provide a very effective and delicate control for the restriction and modification activities of type I systems and its ability to discriminate against DNA restriction in favour of the specific modification of DNA may give some advantage for efficient transmission of the ardA-encoding promiscuous plasmids among different bacterial populations.

Amino Acid Sequence↗
PubMed2001

Characterization of the type IV restriction modification system BspLU11III from Bacillus sp. LU11.

We report the characterization and cloning of the genes for an unusual type IV restriction-modification system, BspLU11III, from Bacillus sp. LU11. The system consists of two methyltransferases and one endonuclease, which also possesses methyltransferase activity. The three genes of the restriction-modification system, bsplu11IIIMa, bsplu11IIIMb and bsplu11IIIR, are closely linked and tandemly arranged. The corresponding enzymes recognize the dsDNA sequence 5'-GGGAC-3'/5'-GTCCC-3', with M.BspLU11IIIa modifying the A (underlined) of one strand and M.BspLU11IIIb the inner C (underlined) of the other strand. R.BspLU11III has both endonuclease and adenine-specific methyltransferase activities and is able to protect the DNA against cleavage by itself. In contrast to all type IV restriction-modification systems described so far, which have only one adenine-specific methyltransferase, BspLU11III is the first type IV restriction-modification system that includes two methyltransferases, one of them being cytosine specific.

Amino Acid Sequence↗
PubMed2004

KpnBI is the prototype of a new family (IE) of bacterial type I restriction-modification system.

KpnBI is a restriction-modification (R-M) system recognized in the GM236 strain of Klebsiella pneumoniae. Here, the KpnBI modification genes were cloned into a plasmid using a modification expression screening method. The modification genes that consist of both hsdM (2631 bp) and hsdS (1344 bp) genes were identified on an 8.2 kb EcoRI chromosomal fragment. These two genes overlap by one base and share the same promoter located upstream of the hsdM gene. Using recently developed plasmid R-M tests and a computer program RM Search, the DNA recognition sequence for the KpnBI enzymes was identified as a new 8 nt sequence containing one degenerate base with a 6 nt spacer, CAAANNNNNNRTCA. From Dam methylation and HindIII sensitivity tests, the methylation loci were predicted to be the italicized third adenine in the 5' specific region and the adenine opposite the italicized thymine in the 3' specific region. Combined with previous sequence data for hsdR, we concluded that the KpnBI system is a typical type I R-M system. The deduced amino acid sequences of the three subunits of the KpnBI system show only limited homologies (25 to 33% identity) at best, to the four previously categorized type I families (IA, IB, IC, and ID). Furthermore, their identity scores to other uncharacterized putative genome type I sequences were 53% at maximum. Therefore, we propose that KpnBI is the prototype of a new 'type IE' family.

Amino Acid Sequence↗
PubMed2026

Post-Translational Modifications in Traumatic Brain Injury: Decoding the Proteomic Landscape and Molecular Mechanisms of Secondary Injury.

Traumatic brain injury (TBI) initiates a complex secondary injury cascade that significantly contributes to long-term neurological deficits, with post-translational modifications (PTMs) emerging as pivotal molecular regulators of this process. Unlike primary mechanical damage, secondary injury evolves over hours to years and involves intricate proteomic alterations that changes in gene expression alone cannot fully explain. PTMs-including phosphorylation, ubiquitination, acetylation, SUMOylation, glycosylation, and emerging modifications such as succinylation, lactylation, and nitrosylation-serve as dynamic molecular switches that fine-tune protein function, stability, localization, and interactions in response to TBI-induced stressors. These modifications play dual roles: they can either promote neuroprotection and recovery or drive pathological processes such as neuronal cell death (via apoptosis, necroptosis, and ferroptosis), neuroinflammation through glial activation and inflammasome signaling, blood-brain barrier disruption, mitochondrial dysfunction, and impaired synaptic plasticity. Critically, extensive crosstalk exists among different PTM pathways-such as the interplay between phosphorylation and ubiquitination in protein degradation or the competitive balance between acetylation and SUMOylation-that collectively shape cellular fate after injury. This nuanced regulatory network presents both challenges and opportunities for therapeutic intervention. Targeting PTM-related enzymes, including kinases, phosphatases, E3 ligases, and histone deacetylases, has shown promise in preclinical models, while novel strategies like Proteolysis-Targeting Chimeras (PROTACs) and repurposed drugs (e.g., metformin, resveratrol) offer innovative avenues for modulating the PTM landscape. Advances in high-throughput proteomics and mass spectrometry are enabling the mapping of TBI-specific PTM signatures across spatiotemporal phases, facilitating the identification of pro-survival versus pro-death modification thresholds. Despite hurdles in clinical translation-such as blood-brain barrier penetration and off-target effects-the growing understanding of PTM dynamics underscores their potential as both biomarkers and therapeutic targets. Future TBI management may thus rely on precision medicine approaches that integrate multi-PTM profiling to guide combination therapies aimed at tipping the balance toward neural repair and functional recovery.

Brain Injuries, Traumatic↗
PubMed1990

Evidence for salt-associated restriction pattern modifications in the archaeobacterium Haloferax mediterranei.

DNA restriction pattern modifications were detected when Haloferax mediterranei was grown in low (10%) salt concentrations. After cells were grown again in optimal (25%) salt concentrations, the original pattern was recovered. These salt-associated DNA modifications were revealed with 5% of the 160 DNA fragments cloned and used as probes in hybridization experiments. Patterns obtained when genomic DNA was digested with different restriction enzymes showed that these modifications are related not to insertions or deletions in genome but to modifications of some specific sequences.

Archaea↗