Structural basis of nucleic acid recognition by the N-terminal cold shock domain of the plant glycine-rich protein AtGRP2.

AtGRP2 is a glycine-rich, RNA-binding protein that plays pivotal roles in abiotic stress response and flowering time regulation in Arabidopsis thaliana. AtGRP2 consists of an N-terminal cold shock domain (CSD) and two C-terminal CCHC-type zinc knuckles interspersed with glycine-rich regions. Here, we investigated the structure, dynamics, and nucleic acid binding properties of AtGRP2-CSD. The 2D [1H,15N] HSQC spectrum of AtGRP2-CSD1-79 revealed the presence of a partially folded intermediate in equilibrium with the folded state. The addition of eleven residues at the C-terminus stabilized the folded conformation. The three-dimensional structure of AtGRP2-CSD1-90 unveiled a ß-barrel composed of five antiparallel ß-strands and a 310 helical turn, along with an ordered C-terminal extension, a conserved feature in eukaryotic CSDs. Direct contacts between the C-terminal extension and the ß3-ß4 loop further stabilized the CSD fold. AtGRP2-CSD1-90 exhibited nucleic acid binding via solvent-exposed residues on strands ß2 and ß3, as well as the ß3-ß4 loop, with higher affinity for DNA over RNA, particularly favoring pyrimidine-rich sequences. Furthermore, DNA binding induced rigidity in the ß3-ß4 loop, evidenced by 15N-{1H} NOE values. Mutation of residues W17, F26, and F37, in the central ß-sheet, completely abolished DNA binding, highlighting the significance of π-stacking interactions in the binding mechanism. These results shed light on the mechanism of nucleic acid recognition employed by AtGRP2, creating a framework for the development of biotechnological strategies aimed at enhancing plant resistance to abiotic stresses.

Spatially resolved distribution of pancreatic hormones proteoforms by MALDI-imaging mass spectrometry.

Zinc plays a crucial role both in the immune system and endocrine processes. Zinc restriction in the diet has been shown to lead to degeneration of the endocrine pancreas, resulting in hormonal imbalance within the ß-cells. Proteostasismay vary depending on the stage of a pathophysiological process, which underscores the need for tools aimed at directly analyzing biological status. Among proteomics methods, MALDI-ToF-MS can serve as a rapid peptidomics tool for analyzing extracts or by histological imaging. Here we report the optimization of MALDI imaging mass spectrometry analysis of histological thin sections from mouse pancreas. This optimization enables the identification of the major islet peptide hormones as well as the major accumulated precursors and/or proteolytic products of peptide hormones. Cross-validation of the identified peptide hormones was performed by LC-ESI-MS from pancreatic islet extracts. Mice subjected to a zinc-restricted diet exhibited a relatively lower amount of peptide intermediates compared to the control group. These findings provide evidence for a complex modulation of proteostasis by micronutrients imbalance, a phenomenon directly accessed by MALDI-MSI.

Zinc deficiency disrupts pain signaling promoting nociceptive but not inflammatory pain in mice.

Zinc (Zn) is an essential micronutrient involved in the physiology of nervous system and pain modulation. There is little evidence for the role of nutritional Zn alternations to the onset and progression of neuropathic (NP) and inflammatory pain. The study investigated the effects of a zinc restricted diet on the development of pain. Weaned mice were submitted to a regular (38 mg/kg of Zn) or Zn deficient (11 mg/kg of Zn) diets for four weeks, pain responses evaluated (mechanical, cold and heat allodynia; formalin- and carrageenan-induced inflammatory hypernociception), plasma and tissues collected for biochemical and metabolomic analysis. Zn deficient diet inhibited animal growth (37%) and changed mice sensitivity pattern, inducing an intense allodynia evoked by mechanical, cold and heat stimulus for four weeks. The inflammatory pain behavior of formalin test was drastically reduced or absent when challenged by an inflammatory stimulus. Zn restriction also reduce plasma TNF, increase neuronal activation, oxidative stress, indicating a disruption of the immune response. Liver metabolomic analyses suggest a downregulation of lipid metabolism of arachidonic acid. Zn restriction since weaned disrupts pain signaling considerably and reduce inflammatory pain. Zn could be considered a predisposing factor for the onset of chronic pain such as painful neuropathies.

Linking B-factor and temperature-induced conformational transition.

The crystallographic B-factor, also called temperature factor or Debye-Waller factor, has long been used as a surrogate for local protein flexibility. However, the use of the absolute B-factor as a probe for protein motion requires reproducible validation against conformational changes against chemical and physical variables. Here we report the investigation of the thermal dependence of the crystallographic B-factor and its correlation with conformational changes of the protein. We obtained the crystal protein structure coordinates and B-factors at high resolution (1.5 Å) over a broad temperature range (100 K to 325 K). The exponential thermal dependence of B-factor as a function of temperature was equal for both the diffraction intensity data (Wilson B-factor) and for all modeled atoms of the system (protein and non-protein atoms), with a thermal diffusion constant of about 0.0045 K-1, similar for all atoms. The extrapolated B-factor at zero Kelvin (or zero-point fluctuation) varies among the atoms, although with no apparent correlation with temperature-dependent protein conformational changes. These data suggest that the thermal vibration of the atom does not necessarily correlate with the conformational dynamics of the protein.

Mutations in asparaginase II from E. coli and implications for inactivation and PEGylation.

All clinically-used asparaginases convert L-asparagine (L-Asn) to l-aspartate (L-Asp) and l-glutamine (L-Gln) to L-glutamate (L-Glu), which has been useful in reducing bioavailable asparagine and glutamine in patients under treatment for acute lymphoblastic leukemia. The E. coli type 2 L-asparaginase (EcA2) can present different sequences among varying bacterial strains, which we hypothesized that might affect their biological function, stability and interchangeability. Here we report the analysis of two EcA2 provided by the public health system of a middle-income country. These enzymes were reported to have similar specific activity in vitro, whereas they differ in vivo. Protein sequencing by LC-MS-MS and peptide mapping by MALDI-ToF-MS of their tryptic digests revealed that Aginasa™ share similar sequence to EcA2 from E. coli strain BL21(DE3), while Leuginase™ has sequence equivalent to EcA2 from E. coli strain AS1.357. The two amino acid differences between Aginasa™ (64D and 252 T) and Leuginase™ (64 N and 252S) resulted in structural divergences in solution as accessed by small-angle X-ray scattering and molecular dynamics simulation trajectories. The conformational variability further results in dissimilar surface accessibility with major consequences for PEGylation, as well as different susceptibility to degradation by limited proteolysis. The present results reveal that the sequence variations between these two EcA2 variants results in conformational changes associated with differential conformational plasticity, potentially affecting physico-chemical and biological properties, including proteolytic and immunogenic silent inactivation.

Formation of subvisible particles in commercial insulin formulations.

The conformation and assembly of insulin are sensitive to physical and chemical variables. Insulin can misfold and form both amorphous and amyloid aggregates. Localized cutaneous amyloidosis due to insulin usage has been reported, and question remains regarding its stability in the original flasks due to storage and handling. Here we report the evaluation of the formation of aggregates in insulin formulations upon once-weekly handling and storage of the in-use cartridges at 4 °C or 37 °C for 5 weeks. Electrospray ionization mass spectrometry showed no obvious chemical decomposition. No major changes in oligomeric distribution were observed by size-exclusion chromatography. Dynamic light scattering allowed the identification of particles with high hydrodynamic radius formed during storage at 4 °C and 37 °C. Transmission electron microscopy analysis revealed the formation of amorphous material, with no clear evidence for amyloid material up to 28 days of incubation. These data support evidences for the formation of subvisible and submicrometer amorphous particulate matter in insulin formulations shortly upon use.

Nutrient-sensing amyloid metastasis.

Amyloids are organized suprastructural polypeptide arrangements. The prevalence of amyloid-related processes of pathophysiological relevance has been linked to aging-related degenerative diseases. Besides the role of genetic polymorphisms on the relative risk of amyloid diseases, the contributions of nongenetic ontogenic cluster of factors remain elusive. In recent decades, mounting evidences have been suggesting the role of essential micronutrients, in particular transition metals, in the regulation of amyloidogenic processes, both directly (such as binding to amyloid proteins) or indirectly (such as regulating regulatory partners, processing enzymes, and membrane transporters). The features of transition metals as regulatory cofactors of amyloid proteins and the consequences of metal dyshomeostasis in triggering amyloidogenic processes, as well as the evidences showing amelioration of symptoms by dietary supplementation, suggest an exaptative role of metals in regulating amyloid pathways. The self- and cross-talk replicative nature of these amyloid processes along with their systemic distribution support the concept of their metastatic nature. The role of amyloidosis as nutrient sensors would act as intra- and transgenerational epigenetic metabolic programming factors determining health span and life span, viability, which could participate as an evolutive selective pressure.

The reproducible normality of the crystallographic B-factor.

Reproducibility determines the utility of a measurement. In structural biology the reproducibility permeate areas such as mechanics, data measurement, data analysis and refinement. In order to access the reproducibility of the combined contribution of these sources in uncertainties of protein crystallography we evaluated four groups of parameters from data collection to final structural model. We used lysozyme as a model, with 20 datasets collected at 1.6 Å resolution using two dissimilar x-ray diffraction setups and refined through a single automatic pipeline without arbitrary interpretation. Besides statistical differences in some structural parameters, the reproducibility of the final refined models allowed the determination of positional uncertainty, in good agreement with the Luzzati coordinate error. While the raw B-factor was found non-reproducible, an empirical scaling/normalization resulted in reproducible B-factors. The validity of this empirical scaling was corroborated by the reproducibility of normalized B-factors of independently solved datasets from proteins (insulin and myoglobin) from varying space groups available from structural database. The reproducibility of normalized B-factor may reposition this displacement parameter in the analysis of chemical (ligands, pH) and physical (pressure, temperature, space groups) variables.

Amyloidogenicity of peptides targeting diabetes and obesity.

Since the discovery of insulin, a century ago, the repertoire of therapeutic polypeptides targeting diabetes - and now also obesity - have increased substantially. The focus on quality has shifted from impure and unstable preparations of animal insulin to highly pure, homologous recombinant insulin, along with other peptide-based hormones and analogs such as amylin analogs (pramlintide, davalintide, cagrilintide), glucagon and glucagon-like peptide-1 receptor agonists (GLP-1, liraglutide, exenatide, semaglutide). Proper formulation, storage, manipulation and usage by professionals and patients are required in order to avoid agglomeration into high molecular weight products (HMWP), either amorphous or amyloid, which could result in potential loss of biological activity and short- or long-term immune reaction and silent inactivation. In this narrative review, we present perspective of the aggregation of therapeutic polypeptides used in diabetes and other metabolic diseases, covering the nature and mechanisms, analytical techniques, physical and chemical stability, strategies aimed to hamper the formation of HMWP, and perspectives on future biopharmaceutical developments.

Polymeric microparticle systems for modified release of glucagon-like-peptide-1 receptor agonists.

Type 2 diabetes is a fast-growing worldwide epidemic. Despite the multiple therapies available to treat type 2 diabetes, the disease is not correctly managed in over half of patients, mainly due to non-compliance with prescribed treatment regimes. The development of analogues to the glucagon-like peptide 1 (GLP-1) has resulted in the extension of its half-life and associated benefits. Further benefits in the use of peptide-based GLP-1 receptor agonists have been achieved by the use of controlled-release systems based on polymeric microparticles. In this review, we focus on commercially available formulations and others that remain in development, discussing the preparation methods and the relationship between in vitro and in vivo kinetic release behaviours.

Biophysical characterization of two commercially available preparations of the drug containing Escherichia coli L-Asparaginase 2.

The hydrolysis of asparagine and glutamine by L-asparaginase has been used to treat acute lymphoblastic leukemia for over four decades. Each L-asparaginase monomer has a long loop that closes over the active site upon substrate binding, acting as a lid. Here we present a comparative study of two commercially available preparations of the drug containing Escherichia coli L-Asparaginase 2 (EcA2), performed by a comprehensive array of biophysical and biochemical approaches. We report the oligomeric landscape and conformational and dynamic plasticity of E. coli type 2 L-asparaginase present in two different formulations, and its relationship with L-aspartic acid, which is present in Aginasa, but not in Leuginase. The L-Asp present in Aginasa formulation was found to provide to EcA2 a resistance to in vitro proteolysis. EcA2 shows a composition of monomers and oligomers up to tetramers, which is mostly not altered in the presence of L-Asp. Ion-mobility spectrometry-mass spectrometry reveals two conformers for the monomeric EcA2, and that monomeric species has sufficient capacity for selective binding to L-Asp and L-Glu. The N-terminal loop of the EcA2 present in Leuginase, which is part of the active site is disordered, but it gets ordered in the presence of L-Asp, while L-Glu only does so to a limited extent. These data provide new insights on the mechanistic of ligand recognition by EcA2, and the impact of formulation in its conformational diversity landscape.

Dietary zinc restriction promotes degeneration of the endocrine pancreas in mice.

Zinc is a key component of several proteins, interacting with the pancreatic hormones insulin and amylin. The role of zinc in insulin oligomerization and crystallinity is well established, although the effects of dietary zinc restriction on both energetic metabolism and ß-pancreatic hormonemia and morphology remain unexplored. Here we report the effects of dietary zinc restriction on the endocrine pancreas and metabolic phenotype of mice. Nontransgenic male Swiss mice were fed a low-zinc or control diet for 4 weeks after weanling. Growth, glycemia, insulinemia and amylinemia were lower and pancreatic islets were smaller in the intervention group despite the preserved insulin crystallinity in secretory granules. We found strong immunostaining for insulin, amylin and oligomers in apoptotic pancreatic islet. High production of ß-pancreatic hormones in zinc-restricted animals counteracted the reduced islet size caused by apoptosis. These data suggest that zinc deficiency is sufficient to promote islet ß-cell hormonal disruption and degeneration.

Heterotropic Modulation of Amylin Fibrillation by Small Molecules: Implications for Formulative Designs.

Control of amylin agglomeration is of interest for both the study of pathophysiology and the design of amylin-based pharmaceutical products. Here we report the effects of a large set of common buffering agents, aminoacids and nucleoside phosphates over the amylin amyloid aggregation. Circular dichroism showed no apparent effects of the co-solutes over the secondary-structure of soluble amylin. Instead, we found a large dependence of the fibrillation process on the total amount of co-solute charged groups. The amyloid nature of the aggregates was confirmed by transmission electron microscopy, X-ray diffraction and infrared spectroscopy. While acidic pH and low-ionic co-solutes shows the largest size effect in hampering aggregation, no further effect was observed that could identify a single compound as a major direct heterotropic determinants of the amyloid process. These data suggest a more physico-chemical effect of co-solutes over the modulation of amylin instead of a chemical entity-related causal factor.

Sustained release and pharmacologic evaluation of human glucagon-like peptide-1 and liraglutide from polymeric microparticles.

The GLP1-receptor agonists exert regulatory key roles in diabetes, obesity and related complications. Here we aimed to develop polymeric microparticles loaded with homologous human GLP1 (7-37) or the analogue liraglutide. Peptide-loaded microparticles were prepared by a double emulsion and solvent evaporation process with a set of eight polymers based on lactide (PLA) or lactide-glycolide (PLGA), and evaluated for particle-size distribution, morphology, in vitro release and pharmacologic activity in mice. The resulting microparticles showed size distribution of about 30-50 µm. The in vitro kinetic release assays showed a sustained release of the peptides extending up to 30-40 days. In vivo evaluation in Swiss male mice revealed a similar extension of glycemic and body weight gain modulation for up to 25 days after a single subcutaneous administration of either hGLP1-microparticles or liraglutide-microparticles. Microparticles-loaded hGLP1 shows equivalent in vivo pharmacologic activity to the microparticles-loaded liraglutide.

Physico-chemical stability of co-formulation of PEGylated human amylin with insulin.

Since the discovery of amylin no combined formulation with insulin has been made available. Amylin or its triple proline analog pramlintide are not compatible in solution with insulin. The drug candidate hAmy-PEG5k is a novel monoPEGylated amylin derivative with improved physicochemical properties and retained similar pharmacological activity compared to free amylin and pramlintide. We have investigated the short- and long-term physicochemical compatibility of hAmy-PEG5k co-formulated with slow-acting human insulin analogs glargine or detemir. While human amylin promptly aggregates over a large range of pH, and both free and in the presence of regular, glargine or detemir insulin, the hAmy-PEG5k analog is stable at these conditions as shown by Thioflavin T (ThT) binding assay. When hAmy-PEG5k (100 or 500 µg/mL) was added to the commercial formulations of either insulin glargine or detemir (95 IU/mL), the combinations remained stable after 6 months stored at 4 °C, as probed by ThT, dynamic light scattering (DLS) measurements and high performance liquid chromatography (HPLC) analyses, confirming the absence of amyloid fibers, minor aggregation products or loss of material. These results suggest hAmy-PEG5k and the insulin analogs glargine and detemir are physicochemically compatible and are candidate ready-to-use fixed-dose combinations.

BZ043, a novel long-acting amylin analog, reduces gastric emptying, food intake, glycemia and insulin requirement in streptozotocin-induced diabetic rats.

Amylin analogs are important adjunctive drugs in the treatment of diabetes mellitus. However, a dual therapy with insulin involves inconvenient multiple injections. Here we describe a novel n-terminal PEGylated human amylin analog - BZ043 - and its potential to improve the control of glycemia using lower doses of insulin. The effect of BZ043 over the insulin-mediated control of fed-glycemia was investigated in rats with streptozotocin-induced diabetes treated with the basal analog glargine (GLAR). Fasted rats (3 h) received a single treatment of BZ043 (16, 64 or 128 nmol/kg), GLAR (1.5 IU or 6.0 IU) or BZ043 plus GLAR low dose (1.5 IU) in separate injections, and had free access to 5% glucose rich chow and water. BZ043 dose-proportionally prevented the meal-related increase of glycemia, and the co-treatment (64 or 128 nmol/kg) with GLAR restored normoglycemia without abrupt variations of glycemia. BZ043 showed a prolonged anti-hyperglycemic effect and, together with GLAR, promoted a long-lasting normoglycemia, in vivo. We conceive that combining BZ043 and GLAR in a fixed-ratio co-formulation might conveniently improve the control of diabetes mellitus.

Oligomeric transition and dynamics of RNA binding by the HuR RRM1 domain in solution.

Human antigen R (HuR) functions as a major post-transcriptional regulator of gene expression through its RNA-binding activity. HuR is composed by three RNA recognition motifs, namely RRM1, RRM2, and RRM3. The two N-terminal RRM domains are disposed in tandem and contribute mostly to HuR interaction with adenine and uracil-rich elements (ARE) in mRNA. Here, we used a combination of NMR and electrospray ionization-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) to characterize the structure, dynamics, RNA recognition, and dimerization of HuR RRM1. Our solution structure reveals a canonical RRM fold containing a 19-residue, intrinsically disordered N-terminal extension, which is not involved in RNA binding. NMR titration results confirm the primary RNA-binding site to the two central ß-strands, ß1 and ß3, for a cyclooxygenase 2 (Cox2) ARE I-derived, 7-nucleotide RNA ligand. We show by 15N relaxation that, in addition to the N- and C-termini, the ß2-ß3 loop undergoes fast backbone dynamics (ps-ns) both in the free and RNA-bound state, indicating that no structural ordering happens upon RNA interaction. ESI-IMS-MS reveals that HuR RRM1 dimerizes, however dimer population represents a minority. Dimerization occurs via the α-helical surface, which is oppositely orientated to the RNA-binding ß-sheet. By using a DNA analog of the Cox2 ARE I, we show that DNA binding stabilizes HuR RRM1 monomer and shifts the monomer-dimer equilibrium toward the monomeric species. Altogether, our results deepen the current understanding of the mechanism of RNA recognition employed by HuR.

Biologically produced silver chloride nanoparticles from B. megaterium modulate interleukin secretion by human adipose stem cell spheroids.

Stem cell tissue constructs are likely to come into contact with silver-based nanoparticles-such as silver chloride nanoparticles (AgCl-NPs)-used as microbicidals at the implant site or in cosmetics. However, the effect of silver-based nanoparticles on 3D cell cultures with potential for tissue engineering has received little attention. Here, we examined the effect of sub-lethal doses (5, 10 and 25 µg/mL, for 1, 7 and 21 days) of AgCl-NPs produced by 'green' bacterial-based synthesis on spheroid 3D cultures of human adipose tissue stem cells (ASCs). Light microscopy analysis revealed that the shape and diameter of ASC spheroids remained largely unchanged after AgCl-NP treatment. Flow cytometry analysis with 7-AAD and 2',7'-dichlorofluorescein diacetate revealed no statistically significant differences in cell death but showed an increase of ROS levels for the untreated group and significant differences for the groups treated with 5 and 10 µg/mL at day 7 (p = 0.0395, p = 0.0266, respectively). Electron microscopy analysis showed limited cell damage in the periphery of AgCl-NP-treated spheroids. However, treatment with AgCl-NP had statistically significant effects on the secretion of IL-6, IL-8, IL-1ß and IL-10 by spheroids, at specific treatment periods and concentrations, and particularly for IL-6, IL-8 and IL-1ß. TGF-ß1 and -ß2 secretion also changed significantly throughout the treatment period. Our results indicate that, despite having little effect on cell viability and morphology, sub-lethal AgCL-NP doses modulate ROS production at day 7 for the groups treated with 5 and 10 µg/mL and also modulate the secretory profile of ASC spheroids. Thus, the use of skin implants or products containing Ag-NPs may promote long-term disturbances in subcutaneous adipose tissue homeostasis.