Post translational modifications of Trifolitoxin: a blue fluorescent peptide antibiotic*

Trifolitoxin (TFX, C41H63N15O15S) is a selective, ribosomally-synthesized, post-translationally modified, peptide antibiotic, produced by Rhizobium leguminosarum bv. trifolii T24. TFX specifically inhibits α-proteobacteria, including the plant symbiont Rhizobium spp., the plant pathogen Agrobacterium spp. and the animal pathogen Brucella abortus. TFX-producing strains prevent legume root nodulation by TFX-sensitive rhizobia. TFX has been isolated as a pair of geometric isomers, TFX1 and TFX2, which are derived from the biologically inactive primary amino acid sequence: Asp-Ile-Gly-Gly-Ser-Arg-Gln-Gly-Cys-Val-Ala. Gly-Cys is present as a thiazoline ring and the Arg-Gln-Gly sequence is extensively modified to a UV absorbing, blue fluorescent chromophore. The chromophore consists of a conjugated, 5-membered heterocyclic ring and side chain of modified glutamine.

βLact-Pred: A Predictor Developed for Identification of Beta-Lactamases Using Statistical Moments and PseAAC via 5-Step Rule

Beta-lactamase (β-lactamase) produced by different bacteria confers resistance against β-lactam-containing drugs. The gene encoding β-lactamase is plasmid-borne and can easily be transferred from one bacterium to another during conjugation. By such transformations, the recipient also acquires resistance against the drugs of the β-lactam family. β-Lactam antibiotics play a vital significance in clinical treatment of disastrous diseases like soft tissue infections, gonorrhoea, skin infections, urinary tract infections, and bronchitis. Herein, we report a prediction classifier named as βLact-Pred for the identification of β-lactamase proteins. The computational model uses the primary amino acid sequence structure as its input. Various metrics are derived from the primary structure to form a feature vector. Experimentally determined data of positive and negative beta-lactamases are collected and transformed into feature vectors. An operating algorithm based on the artificial neural network is used by integrating the position relative features and sequence statistical moments in PseAAC for training the neural networks. The results for the proposed computational model were validated by employing numerous types of approach, i.e., self-consistency testing, jackknife testing, cross-validation, and independent testing. The overall accuracy of the predictor for self-consistency, jackknife testing, cross-validation, and independent testing presents 99.76%, 96.07%, 94.20%, and 91.65%, respectively, for the proposed model. Stupendous experimental results demonstrated that the proposed predictor “βLact-Pred” has surpassed results from the existing methods.

CVID-Associated B Cell Activating Factor Receptor Variants Change Receptor Oligomerization, Ligand Binding and Signaling Responses

Purpose B cell activating factor (BAFF) binding to BAFF-receptor(BAFFR) activates essential cellular functions required forthe survival of mature, human B cells. Thus,deletion ofthe BAFFR gene blocks the development of B cells at the transition from immature to mature B cells resulting in B lymphopenia and hypogammaglobulinemia. In addition to complete BAFFR deficiency, single nucleotide variants changing the primary amino acid sequence of BAFFR gene exist. Some of these variants were foundin patients suffering from immunodeficiency, autoimmunity, or B cell lymphomas. However, it remains unclearto which extent such variants disturb the activity of BAFFR. Methods Since individual differences and genetic/environmental modifiers change the expression and activity of BAFFR, we developed a cellular system that allows the unbiased analysis of BAFFR variants P21R, A52T, G64V, Dup92-95, P146S, and H159Y regarding oligomerization, signaling, and ectodomain shedding.Results Here we show that several of these variants impair BAFFR oligomerization, direct interactions between BAFFR and the B cell receptor component CD79B, BAFFR ectodomain shedding and the activation of AKT and ERK1/2. Conclusion All of these variants are pathogenic and have the potential to contribute to the development of primary antibody deficiencies, autoimmunity and lymphoma, but they most likely do not cause B lymphopenia and agammaglobulinemia like complete BAFFR deficiency.

The Making and Breaking of Serine-ADP-Ribosylation in the DNA Damage Response

ADP-ribosylation is a widespread posttranslational modification that is of particular therapeutic relevance due to its involvement in DNA repair. In response to DNA damage, PARP1 and 2 are the main enzymes that catalyze ADP-ribosylation at damage sites. Recently, serine was identified as the primary amino acid acceptor of the ADP-ribosyl moiety following DNA damage and appears to act as seed for chain elongation in this context. Serine-ADP-ribosylation strictly depends on HPF1, an auxiliary factor of PARP1/2, which facilitates this modification by completing the PARP1/2 active site. The signal is terminated by initial poly(ADP-ribose) chain degradation, primarily carried out by PARG, while another enzyme, (ADP-ribosyl)hydrolase 3 (ARH3), specifically cleaves the terminal seryl-ADP-ribosyl bond, thus completing the chain degradation initiated by PARG. This review summarizes recent findings in the field of serine-ADP-ribosylation, its mechanisms, possible functions and potential for therapeutic targeting through HPF1 and ARH3 inhibition.

High-resolution capillary electrophoresis for the determination of carbamylated albumin

Objectives Carbamylation is a non-enzymatic post-translational reaction of a primary amino group of a protein with isocyanate. The albumin carbamylation is a negative prognostic factor in chronic kidney disease (CKD) patients and induce charge difference implying an observed shift in electrophoretic mobility that can be measured through a symmetry factor (SF). Methods The Helena V8 and the Sebia Capillarys 2 systems were used for all experiments. The effect of in vitro carbamylation on the SF by spiking increasing concentrations of potassium isocyanate (KCNO) in serum of three healthy volunteers was investigated. Theoretical plate numbers (N) as a surrogate of separation efficiency were also calculated and correlations between SF and renal function biomarkers were performed on 284 patients. Results A dose-dependent impact of KCNO on the SF was observed for both methods with the Helena V8 being more sensitive. The mean N was significantly higher on the Helena V8 as compared to the Sebia Capillarys 2 (2,972 vs. 444.1, p<0.0001). The SF correlated significantly with eGFR (r=0.50, p<0.0001), creatinine (r=−0.31, p<0.0001) and urea (r=−0.34, p<0.0001) on the Helena V8. On the Sebia Capillarys 2, a significant correlation was only observed with eGFR (r=0.17, p=0.004). A better discrimination between CKD stages was also observed using the Helena V8. Conclusions Thanks to a higher mean N, the Helena V8 might offer new possibilities, including detection of carbamylated albumin through SF calculation. Further studies are still needed to confirm the interest of using this type of assays in clinical routine.

Laccase-Catalyzed Derivatization of Antibiotics with Sulfonamide or Sulfone Structures

Trametes spec. laccase (EC 1.10.3.2.) mediates the oxidative coupling of antibiotics with sulfonamide or sulfone structures with 2,5-dihydroxybenzene derivatives to form new heterodimers and heterotrimers. These heteromolecular hybrid products are formed by nuclear amination of the p-hydroquinones with the primary amino group of the sulfonamide or sulfone antibiotics, and they inhibited in vitro the growth of Staphylococcus species, including multidrug-resistant strains.

Spectrophotometric methods for the determination of lisinopril in medicines

Two simple, rapid and green spectrophotometric methods are described for the determination of lisinopril medicines. The determination is based on the reaction of the primary amino group of the lisinopril with ninhydrin in aqueous medium (Method I) and reaction on the carboxylic group of the lisinopril with copper (II) sulfate (Method II). For both methods, optimal spectrophotometric conditions were established. The linear relationship was found between absorbance at λmax and concentration of drug in the range 40–60 µg/mL (Method I) and 0.592–2.072 mg/mL (Method II). Regression analysis of Beer’s law plot at 400 nm yielded the regression equation, y = 7.4929x – 0.0545 (Method I) and at 730 nm y = 0.0443x – 0.0832 (Method II). High values of correlations coefficient (R2 = 0.9917 (Method I) and R2 = 0.999 (Method II)) and small values of intercept validated the linearity of calibration curve and obedience to Beer’s law. The LOD and LOQ values were calculated to be 6.91 µg/mL and 23.01 µg/mL respectively (Method I) and 0.11 mg/mL and 0.36 mg/mL respectively (Method II). Intra-day and inter-day accuracy and precision were in acceptable limits. The proposed methods were applied for the quantification of lisinopril in tablets pertaining to three commercial formulations. Analytical eco-scale for greenness assessment of the proposed spectrophotometric methods showed that both methods correspond to excellent green analysis.

Selected Applications of Chitosan Composites

Chitosan is one of the emerging materials for various applications. The most intensive studies have focused on its use as a biomaterial and for biomedical, cosmetic, and packaging systems. The research on biodegradable food packaging systems over conventional non-biodegradable packaging systems has gained much importance in the last decade. The deacetylation of chitin, a polysaccharide mainly obtained from crustaceans and shrimp shells, yields chitosan. The deacetylation process of chitin leads to the generation of primary amino groups. The functional activity of chitosan is generally owed to this amino group, which imparts inherent antioxidant and antimicrobial activity to the chitosan. Further, since chitosan is a naturally derived polymer, it is biodegradable and safe for human consumption. Food-focused researchers are exploiting the properties of chitosan to develop biodegradable food packaging systems. However, the properties of packaging systems using chitosan can be improved by adding different additives or blending chitosan with other polymers. In this review, we report on the different properties of chitosan that make it suitable for food packaging applications, various methods to develop chitosan-based packaging films, and finally, the applications of chitosan in developing multifunctional food packaging materials. Here we present a short overview of the chitosan-based nanocomposites, beginning with principal properties, selected preparation techniques, and finally, selected current research.

Evaluation and Implementation of Biocompatible Methods for the Cross-linking of Plasma Proteins

Autologous plasma proteins can be used to fabricate patient specific cardiovascular implants but need to be cross-linked to increase their mechanical strength and reduce water solubility. Glutaraldehyde is the state-of-the-art solution but its reaction products have been shown to be cytotoxic and pro-inflammatory. In this work, it has been shown, that cross-linking of plasma proteins with biocompatible alternatives to glutaraldehyde is possible. This was achieved by identifying four candidate substances (thrombin, transglutaminase, genipin, EDC) from current literature and investigating their ability to cross-link porcine plasma proteins in vitro. The degree of crosslinking was examined using calorimetric (DSC) and spectroscopic (FTIR, Raman) methods, mapping the influence of cross-linking on the denaturation temperature and primary amino-group content of the proteins. It could be shown that thrombin, genipin and EDC are able to cross-link plasma proteins to a satisfactory degree and thus represent useful alternatives to glutaraldehyde. Transglutaminase, on the other hand, could not sufficiently cross-link the plasma proteins and was therefore ruled out as an alternative.

Interaction of Linear Polyelectrolytes with Proteins: Role of Specific Charge–Charge Interaction and Ionic Strength

We present a thermodynamic study of the interaction of synthetic, linear polyelectrolytes with bovine serum albumin (BSA). All polyelectrolytes are based on poly(allyl glycidyl ether) which has been modified by polymer-analogous reaction with anionic (-SO3Na), cationic (-NH3Cl or -NHMe2Cl) or zwitterionic groups (-NMe2(CH2)3SO3). While the anionic polymer shows a very weak interaction, the zwitterionic polymer exhibits no interaction with BSA (pI = 4.7) under the applied pH = 7.4, ionic strength (I = 23–80 mM) and temperature conditions (T = 20–37 °C). A strong binding, however, was observed for the polycations bearing primary amino or tertiary dimethyl amino groups, which could be analysed in detail by isothermal titration calorimetry (ITC). The analysis was done using an expression which describes the free energy of binding, DGb, as the function of the two decisive variables, temperature, T, and salt concentration, cs. The underlying model splits DGb into a term related to counterion release and a term related to water release. While the number of released counter ions is similar for both systems, the release of bound water is more important for the primary amine compared to the tertiary N,N-dimethyl amine presenting polymer. This finding is further traced back to a closer contact of the polymers’ protonated primary amino groups in the complex with oppositely charged moieties of BSA as compared to the bulkier protonated tertiary amine groups. We thus present an investigation that quantifies both driving forces for electrostatic binding, namely counterion release and change of hydration, which contribute to a deeper understanding with direct impact on future advancements in the biomedical field.