Chemoselective Labeling and Immobilization of Phosphopeptides with Phosphorimidazolide Reagents

Protein phosphorylation is one of the most ubiquitous post-translational modifications, regulating numerous essential processes in cells. Accordingly, the large-scale annotation of phosphorylation sites continues to provide central insight into the regulation of signaling networks. The global analysis of the phosphoproteome typically relies on mass spectrometry analysis of phosphopeptides, with an enrichment step necessary due to the sub-stoichiometric nature of phosphorylation. Several affinity-based methods and chemical modification strategies have been developed to date, but the choice of enrichment method can have a considerable impact on the results. Here, we show that a biotinylated, photo-cleavable phosphorimidazolide reagent permits the immobilization and subsequent cleavage of phosphopeptides. The method is capable of the capture and release of phosphopeptides of varying characteristics, and this mild and selective strategy expands the current repertoire for phosphopeptide chemical modification with the potential to enrich and identify new phosphorylation sites in the future.

Combined Structural Analysis and Molecular Dynamics Reveal Penicillin-Binding Protein Inhibition Mode with β-Lactones

β-Lactam antibiotics comprise one of the most widely used therapeutic classes to combat bacterial infections. This general scaffold has long been known to inhibit bacterial cell wall biosynthesis by inactivating penicillin-binding proteins (PBPs); however, bacterial resistance to β-lactams is now widespread, and new strategies are urgently needed to target PBPs and other proteins involved in bacterial cell wall formation. A key requirement in the identification of strategies to overcome resistance is a deeper understanding of the roles of the PBPs and their associated proteins during cell growth and division, such as can be obtained with the use of selective chemical probes. Probe development has typically depended upon known PBP inhibitors, which have historically been thought to require a negatively charged moiety that mimics the C-terminus of the PBP natural peptidoglycan substrate, d-Ala-d-Ala. However, we have identified a new class of β-lactone-containing molecules that interact with PBPs, often in an isoform-specific manner, and do not incorporate this C-terminal mimetic. Here, we report a series of structural biology experiments and molecular dynamics simulations that we utilized to evaluate specific binding modes of this novel PBP inhibitor class. In this work, we obtained <2 Å resolution X-ray structures of four β-lactone probes bound to PBP1b from Streptococcus pneumoniae. Despite their diverging recognition modes beyond the site of covalent modification, these four probes all efficiently labeled PBP1b, as well as other PBPs from S. pneumoniae. From these structures, we analyzed protein-ligand interactions and characterized the β-lactone-bound active sites using in silico mutagenesis and molecular dynamics. Our approach has clarified the dynamic interaction profile in this series of ligands, expanding the understanding of PBP inhibitor binding.

Affinity-based proteomics reveals novel targets of inositol pyrophosphate (5-IP7 )-dependent phosphorylation and binding in Trypanosoma cruzi replicative stages

Diphosphoinositol-5-pentakisphosphate (5-PP-IP₅ ), also known as inositol heptakisphosphate (5-IP₇ ), has been described as a high-energy phosphate metabolite that participates in the regulation of multiple cellular processes through protein binding or serine pyrophosphorylation, a posttranslational modification involving a β-phosphoryl transfer. In this study, utilizing an immobilized 5-IP₇ affinity reagent, we performed pull-down experiments coupled with mass spectrometry identification, and bioinformatic analysis, to reveal 5-IP₇ -regulated processes in the two proliferative stages of the unicellular parasite Trypanosoma cruzi. Our protein screen clearly defined two cohorts of putative targets either in the presence of magnesium ions or in metal-free conditions. We endogenously tagged four protein candidates and immunopurified them to assess whether 5-IP₇ -driven phosphorylation is conserved in T. cruzi. Among the most interesting targets, we identified a choline/o-acetyltransferase domain-containing phosphoprotein that undergoes 5-IP₇ -mediated phosphorylation events at a polyserine tract (Ser^578-580 ). We also identified a novel SPX domain-containing phosphoribosyltransferase [EC 2.7.6.1] herein termed as TcPRPPS4. Our data revealed new possible functional roles of 5-IP₇ in this divergent eukaryote, and provided potential new targets for chemotherapy.

Comparison of Bioorthogonal β-Lactone Activity-Based Probes for Selective Labeling of Penicillin-Binding Proteins

Penicillin-binding proteins (PBPs) are a family of bacterial enzymes that are key components of cell-wall biosynthesis and the target of β-lactam antibiotics. Most microbial pathogens contain multiple structurally homologous PBP isoforms, making it difficult to target individual PBPs. To study the roles and regulation of specific PBP isoforms, a panel of bioorthogonal β-lactone probes was synthesized and compared. Fluorescent labeling confirmed selectivity, and PBPs were selectively enriched from Streptococcus pneumoniae lysates. Comparisons between fluorescent labeling of probes revealed that the accessibility of bioorthogonal reporter molecules to the bound probe in the native protein environment exerts a more significant effect on labeling intensity than the bioorthogonal reaction used, observations that are likely applicable beyond this class of probes or proteins. Selective, bioorthogonal activity-based probes for PBPs will facilitate the activity-based determination of the roles and regulation of specific PBP isoforms, a key gap in knowledge that has yet to be filled.

British Journal of Biomedical Science in 2020. What have we learned?

Each year the British Journal of Biomedical Science publishes a 'What have we learned' editorial designed to introduce readers within the major disciplines of laboratory medicine to developments outside their immediate area. In addition it is designed to inform a wider readership of the advances in the diagnosis and treatment of disease. To this end, in 2020 the journal published 39 articles covering the disciplines within Biomedical Science in the 4 issues comprising volume 77. These included a review of COVID-19 in this issue, 27 original articles, 6 Biomedical Science 'In Brief' and 4 case histories. 27 of the articles involved molecular techniques, with one of these comparing results with a mass spectrometry based method. The preponderance of molecular genetic studies gives us a good idea of the likely future direction of the disciplines.

Chemical tools for selective activity profiling of bacterial penicillin-binding proteins

Penicillin-binding proteins (PBPs) are membrane-associated proteins involved in the biosynthesis of peptidoglycan (PG), the main component of bacterial cell walls. These proteins were discovered and named for their affinity to bind the β-lactam antibiotic penicillin. The importance of the PBPs has long been appreciated; however, specific roles of individual family members in each bacterial strain, as well as their protein-protein interactions, are yet to be understood. The apparent functional redundancy of the 4-18 PBPs that most eubacteria possess makes determination of their individual roles difficult. Existing techniques to study PBPs are not ideal because they do not directly visualize protein activity and can suffer from artifacts and perturbations of native PBP function. Therefore, development of new methods for studying the roles of individual PBPs in cell wall synthesis is required. We recently generated a library of fluorescent chemical probes containing a β-lactone scaffold that specifically targets the PBPs, enabling the visualization of their catalytic activity. Herein, we describe a general protocol to label and detect the activity of individual PBPs in Streptococcus pneumoniae using our fluorescent β-lactone probes.

MLKL Requires the Inositol Phosphate Code to Execute Necroptosis

Necroptosis is an important form of lytic cell death triggered by injury and infection, but whether mixed lineage kinase domain-like (MLKL) is sufficient to execute this pathway is unknown. In a genetic selection for human cell mutants defective for MLKL-dependent necroptosis, we identified mutations in IPMK and ITPK1, which encode inositol phosphate (IP) kinases that regulate the IP code of soluble molecules. We show that IP kinases are essential for necroptosis triggered by death receptor activation, herpesvirus infection, or a pro-necrotic MLKL mutant. In IP kinase mutant cells, MLKL failed to oligomerize and localize to membranes despite proper receptor-interacting protein kinase-3 (RIPK3)-dependent phosphorylation. We demonstrate that necroptosis requires IP-specific kinase activity and that a highly phosphorylated product, but not a lowly phosphorylated precursor, potently displaces the MLKL auto-inhibitory brace region. These observations reveal control of MLKL-mediated necroptosis by a metabolite and identify a key molecular mechanism underlying regulated cell death.

Chemical tools for interrogating inositol pyrophosphate structure and function

The inositol pyrophosphates (PP-InsPs) are a unique group of intracellular messengers that represent some of the most highly phosphorylated molecules in nature. Genetic perturbation of the PP-InsP biosynthetic network indicates a central role for these metabolites in maintaining cellular energy homeostasis and in controlling signal transduction networks. However, despite their discovery over two decades ago, elucidating their physiologically relevant isomers, the biochemical pathways connecting these molecules to their associated phenotypes, and their modes of signal transduction has often been stymied by technical challenges. Many of the advances in understanding these molecules to date have been facilitated by the total synthesis of the various PP-InsP isomers and by the development of new methods that are capable of identifying their downstream signalling partners. Chemical tools have also been developed to distinguish between the proposed PP-InsP signal transduction mechanisms: protein binding, and a covalent modification of proteins termed protein pyrophosphorylation. In this article, we review these recent developments, discuss how they have helped to illuminate PP-InsP structure and function, and highlight opportunities for future discovery.

Cellular Cations Control Conformational Switching of Inositol Pyrophosphate Analogues

The inositol pyrophosphate messengers (PP-InsPs) are emerging as an important class of cellular regulators. These molecules have been linked to numerous biological processes, including insulin secretion and cancer cell migration, but how they trigger such a wide range of cellular responses has remained unanswered in many cases. Here, we show that the PP-InsPs exhibit complex speciation behaviour and propose that a unique conformational switching mechanism could contribute to their multifunctional effects. We synthesised non-hydrolysable bisphosphonate analogues and crystallised the analogues in complex with mammalian PPIP5K2 kinase. Subsequently, the bisphosphonate analogues were used to investigate the protonation sequence, metal-coordination properties, and conformation in solution. Remarkably, the presence of potassium and magnesium ions enabled the analogues to adopt two different conformations near physiological pH. Understanding how the intrinsic chemical properties of the PP-InsPs can contribute to their complex signalling outputs will be essential to elucidate their regulatory functions.

Disinfection of water by adsorption combined with electrochemical treatment

The disinfection performance of a unique process of adsorption combined with electrochemical treatment is evaluated. A flake graphite intercalation compound adsorbent was used, which is effective for the removal of organic contaminants and is amenable to anodic electrochemical regeneration. Adsorption of Escherichia coli on the graphite flake was followed by electrochemical treatment under a range of experimental conditions in a sequential batch reactor. The adsorption of E. coli cells was found to be a fast process and was capable of removing >99.98% of cells from solution after 5 min with a ca. 6.5-log10 reduction in E. coli concentration after 10 min. With electrochemical treatment the adsorbent could be reused, with no decrease in E. coli adsorption observed over five cycles. In the presence of chloride, >8.5-log10 reduction of E. coli concentration was achieved. Disinfection was found to be less effective in the absence of chloride. However, selection of appropriate operating conditions enabled effective disinfection in a chloride free system, reducing the potential for formation of disinfection by-products. The energy consumption required to achieve >8.5-log10 disinfection was 2-7 kWh m(-3).

High-affinity recognition of HIV-1 frameshift-stimulating RNA alters frameshifting in vitro and interferes with HIV-1 infectivity

The life cycle of the human immunodeficiency virus type 1 (HIV-1) has an absolute requirement for ribosomal frameshifting during protein translation in order to produce the polyprotein precursor of the viral enzymes. While an RNA stem-loop structure (the “HIV-1 Frameshift Stimulating Signal”, or HIV-1 FSS) controls the frameshift efficiency and has been hypothesized as an attractive therapeutic target, developing compounds that selectively bind this RNA and interfere with HIV-1 replication has proven challenging. Building on our prior discovery of a “hit” molecule able to bind this stem-loop, we now report the development of compounds displaying high affinity for the HIV-1 FSS. These compounds are able to enhance frameshifting more than 50% in a dual-luciferase assay in human embryonic kidney cells, and they strongly inhibit the infectivity of pseudotyped HIV-1 virions.

Combining adsorption with anodic oxidation as an innovative technique for removal and destruction of organics

Coupling of adsorption with electrochemical oxidation is a novel approach to the treatment of aqueous organics that has demonstrated a number of key benefits over the individual application of these processes. This is based on a highly conducting adsorbent material, developed under the trade name Nyex™, that is able to rapidly adsorb the organics and anodically oxidise them within a single treatment unit. Successful scale up of the process (in both continuous and batch operation) has been achieved for the polishing of two separate groundwaters (one containing relatively simple petrol, diesel and their degradation products and the other with a range of more complex organics). Treatment showed that low discharge consents can be achieved, including the removal of more complex and difficult to treat compounds to below the limits of detection. Energy consumption for electrochemical regeneration was relatively low (down to 0.5 kWh/m(3)) suggesting that the process could be a practical alternative approach for effluent polishing.

Removal of mercaptans from a gas stream using continuous adsorption-regeneration

The removal of the mercaptan, 1-methyl-1-propanethiol, from aqueous solutions using a non-porous, electrically conducting carbon-based adsorbent (Nyex 1000) was investigated. The adsorption process was found to be rapid (equilibrium capacity achieved within 5 minutes) with low adsorptive capacity (of the order of 0.4 mg g(-1)) when compared with activated carbon. Electrochemical regeneration of the Nyex 1000 in a simple divided electrochemical cell within a sequential batch treatment unit restored 100% of the adsorbent's adsorptive capacity using treatment times as low as 20 minutes by passing a current of 0.5 A. The sorptive characteristics of a Nyex-water slurry were also modelled and investigated both in a bubble column and in a continuous adsorption-regeneration treatment system. It was demonstrated that the continuous removal-destruction system could achieve a step reduction in challenge gas concentration of approximately 75% for a period of 35 minutes with a current of 5 Amps. This was attributed to mass transfer enhanced by a combination of adsorption and chemical reaction with free chlorine species generated in the electrochemical process.

Continuous water treatment by adsorption and electrochemical regeneration

This study describes a process for water treatment by continuous adsorption and electrochemical regeneration using an air-lift reactor. The process is based on the adsorption of dissolved organic pollutants onto an adsorbent material (a graphite intercalation compound, Nyex(®)1000) and subsequent electrochemical regeneration of the adsorbent leading to oxidation of the adsorbed pollutant. Batch experiments were carried out to determine the adsorption kinetics and equilibrium isotherm for adsorption of a sample contaminant, the organic dye Acid Violet 17. The adsorbent circulation rate, the residence time distribution (RTD) of the reactor, and treatment by continuous adsorption and electrochemical regeneration were studied to investigate the process performance. The RTD behaviour could be approximated as a continuously stirred tank. It was found that greater than 98% removal could be achieved for continuous treatment by adsorption and electrochemical regeneration for feed concentrations of up to 300 mg L(-1). A steady state model has been developed for the process performance, assuming full regeneration of the adsorbent in the electrochemical cell. Experimental data and modelled predictions (using parameters for the adsorbent circulation rate, adsorption kinetics and isotherm obtained experimentally) of the dye removal achieved were found to be in good agreement.

Atrazine removal using adsorption and electrochemical regeneration

This paper demonstrates the removal of atrazine using a novel carbon-based adsorbent to below 1.0 microg l(-1) and its subsequent electrochemical regeneration in a simple electrochemical cell. Effective electrochemical regeneration can be achieved with a treatment time as low as 20 min over a number of adsorption/regeneration cycles using laboratory-prepared solutions. The results suggest that electrochemical modification of the particulate surface on electrochemical regeneration can result in adsorptive capacities three times greater than originally achieved.

Treatment of dyehouse effluents with a carbon-based adsorbent using anodic oxidation regeneration

Adsorption is an attractive route for the removal of coloured, toxic and non-biodegradable organics from wastewater as very low discharge standards can be achieved. This paper reports on the use of a novel carbon-based material, Nyex100, as an adsorbent material for the treatment of dyehouse effluent. The adsorbent has low porosity and high electrical conductivity and these factors have allowed the adsorbent to be electrochemically regenerated. This work has demonstrated that the adsorbent can be cycled through the process of adsorption and regeneration a number of times with little drop in adsorptive capacity. However regeneration appears to modify the preference for organic species adsorption. Electrochemical regeneration can be rapidly achieved (15-20 minutes) using low current densities (< 20 mA cm(-2)). However, the low adsorptive capacity of the adsorbent, because of its small surface area, means that large quantities of adsorbent would need to be cycled within the process to treat the effluent volume generated in even small dyehouses. Thus, it is believed that operating the process in this mode limits the practical application of this technology.

Anaesthetic considerations in a parturient with varicella presenting for Caesarean section

A parturient with varicella (chickenpox) presented for an elective Caesarean section and spinal anaesthesia was employed for surgery. A review of the literature is presented and the anaesthetic issues are discussed.

Evidence for long-term pancreatic damage caused by laxative abuse in subjects recovered from anorexia nervosa

OBJECTIVE

This study examined whether a prior history of laxative abuse results in long-term changes in gastrointestinal function.

METHOD

The functioning of the enteroinsular axis was examined by measuring the insulin response to a standard meal. The study involved 18 subjects who had fully recovered from anorexia nervosa (AN) and an age and weight-matched control group. In the recovered group, 10 of 18 subjects had a history of laxative abuse.

RESULTS

Subjects with a prior history of laxative abuse show a more gradual increase and decrease in insulin secretion, but no differences in glucose response or hunger ratings.

DISCUSSION

Because there are no differences in the glucose response to the meal, it is hypothesized that the difference in insulin response is due to changes in the enteroinsular axis. These data indicate that chronic laxative abuse induces long-term changes in gastrointestinal function.

Anorexia nervosa visited and revisited: weight is the issue

Anorexia nervosa is known as a psychiatric disorder. Many practitioners seem unaware that a patient in a starvation state is cognitively impaired and thus a poor candidate for psychotherapy. Weight restoration is a prerequisite to other treatment modalities. Many practitioners and all patients fail to recognize this illness because of a prevailing cultural idealization of thinness. Since these patients initially seem so compliant in treatment, valuable time is lost by those who fail to understand the patient's deceptiveness and the life-threatening potential of the disease.

Comparison of described empathic and nominated empathic individuals

A composite profile of "empathic individuals" was developed from adjectives checked on Gough and Heilbrun's Adjective Check List by 43 undergraduate students enrolled in a course on counseling. Individuals were nominated as empathic by the students who also completed the checklist. The composite profile was consistent with the Rogerian definition of empathy and Factor 3 (Sociability) of the check list. The profiles for the nominated sample and for the students did not differ significantly on 36 of the 37 scales but both differed significantly from the composite profile on 34 scales.

Empathy scores of nurses, psychiatrists and hospital administrators on the California Psychological Inventory

12 medical-surgical nurses, 12 psychiatric nurses, 10 intensive care nurses, 10 hospital administrators, and 10 psychiatrists were administered the California Psychological Inventory. Protocols were scored for 18 scales plus Hogan's Empathy Scale. Significant differences were found between groups and the medical-surgical nurses scored lowest on all scales. The scores for all groups were combined and correlations between the Empathy Scale and other CPI scales were computed. Factor 2 scales, Interpersonal Adequacy, scores had the highest correlations with the Empathy Scale.

Assessment measures that discriminate between levels of DUI clients

The Adjective Checklist, Multiple Affect Adjective Checklist, Depression Adjective Checklist, and Profile of Mood States were administered to 166 males enrolled in an Alcohol Safety Action Program. Although a few individual scales showed significant differences between groups, a stepwise multiple discriminant analysis of combined test scales identified two functions, Intrapersonal Attributes which accounted for 84% of the variance and Personal Adequacy, accounting for 15.9% of the variance. The combined test results correctly classified 62% of the clients. Cross-validation is planned.

Medical consequences of eating disorders

While much has appeared in the recent literature about various psychotherapeutic techniques used to treat eating disorders, little attention has been paid to the medical complications. Prominent among these are heart damage, failure of the endocrine system, infarction and perforation of the stomach after acute dilatation, multiple suicide attempts, aspiration, injury or rupture of the esophagus, severe bleeding per rectum causing anemia due to laxative abuse, hypokalemic nephropathy, depressive disorders due to starvation, and severe erosion of the enamel of the teeth resulting in extensive loss of teeth. I decry the sudden trend of nonmedically trained personnel rushing into the treatment of eating disorders, particularly anorexia nervosa and bulimia, because they know little about the possibly fatal consequences of their failure to attend to some of these medical phenomena. I also note with grave concern the identification of the medical profession with the "thin is better" mentality of our culture, which blinds them to the serious medical consequences of eating disorders.