Crowding within synaptic junctions influences the degradation of nucleotides by CD39 and CD73 ectonucleotidases.

Synapsed cells can communicate using exocytosed nucleotides like adenosine triphosphate (ATP). Ectonucleotidases localized to synaptic junctions degrade nucleotides into metabolites like adenosine monophosphate (AMP) or adenosine. Oftentimes nucleotide degradation occurs in a sequential manner, of which ATP degradation by CD39 and CD73 is a representative example. Here, CD39 first converts ATP and adenosine diphosphate (ADP) into AMP, after which AMP is dephosphorylated into adenosine by CD73. Hence, the concerted activity of CD39 and CD73 can help shape cellular responses to extracellular ATP. In a previous study, we demonstrated that coupled CD39 and CD73 activity within synapse-like junctions is strongly controlled by the enzymes' co-localization, their surface charge densities, and the electrostatic potential of the surrounding cell membranes. In this study, we demonstrate that crowders within synaptic junctions, which can include globular proteins like cytokines and membrane-bound proteins, impact coupled CD39 and CD73 ectonucleotidase activity and, in turn, the availability of intrasynapse ATP. Specifically, we developed a spatially explicit, reaction-diffusion model for the coupled conversion of ATP → AMP and AMP → adenosine in a model synaptic junction with crowders that is solved via the finite element method. Our modeling results suggest that the association rate for ATP to CD39 is strongly influenced by the density of intrasynaptic protein crowders, as increasing crowder density generally suppressed ATP association kinetics. Much of this suppression can be rationalized based on a loss of configurational entropy. The surface charges of crowders can further influence the association rate, with the surprising result that favorable crowder-nucleotide electrostatic interactions can yield CD39 association rates that are faster than crowder-free configurations. However, attractive crowder-nucleotide interactions decrease the rate and efficiency of adenosine production, which in turn increases the availability of ATP and AMP within the synapse relative to crowder-free configurations. These findings highlight how CD39 and CD73 ectonucleotidase activity, electrostatics, and crowding within synapses influence the availability of nucleotides for intercellular communication.

Simulation of P2X-mediated calcium signalling in microglia.

KEY POINTS: A computational model of P2X channel activation in microglia was developed that includes downfield Ca2+ -dependent signalling pathways. This model provides quantitative insights into how diverse signalling pathways in microglia converge to control microglial function. ABSTRACT: Microglia function is orchestrated through highly coupled signalling pathways that depend on calcium (Ca2+ ). In response to extracellular ATP, transient increases in intracellular Ca2+ driven through the activation of purinergic receptors, P2X and P2Y, are sufficient to promote cytokine synthesis. Although the steps comprising the pathways bridging purinergic receptor activation with transcriptional responses have been probed in great detail, a quantitative model for how these steps collectively control cytokine production has not been established. Here we developed a minimal computational model that quantitatively links extracellular stimulation of two prominent ionotropic purinergic receptors, P2X4 and P2X7, with the graded production of a gene product, namely the tumour necrosis factor α (TNFα) cytokine. In addition to Ca2+ handling mechanisms common to eukaryotic cells, our model includes microglia-specific processes including ATP-dependent P2X4 and P2X7 activation, activation of nuclear factor of activated T-cells (NFAT) transcription factors, and TNFα production. Parameters for this model were optimized to reproduce published data for these processes, where available. With this model, we determined the propensity for TNFα production in microglia, subject to a wide range of ATP exposure amplitudes, frequencies and durations that the cells could encounter in vivo. Furthermore, we have investigated the extent to which modulation of the signal transduction pathways influence TNFα production. Our results suggest that pulsatile stimulation of P2X4 via micromolar ATP may be sufficient to promote TNFα production, whereas high-amplitude ATP exposure is necessary for production via P2X7. Furthermore, under conditions that increase P2X4 expression, for instance, following activation by pathogen-associated molecular factors, P2X4-associated TNFα production is greatly enhanced. Given that Ca2+ homeostasis in microglia is profoundly important to its function, this computational model provides a quantitative framework to explore hypotheses pertaining to microglial physiology.

Dissipative particle dynamics simulation study of poly(2-oxazoline)-based multicompartment micelle nanoreactor.

We investigate multicompartment micelles consisting of poly(2-oxazoline)-based triblock copolymers for nanoreactor applications, using the DPD simulation method to characterize the internal structure of the micelles and the distribution of reactant. The DPD simulation parameters are determined from the Flory-Huggins interaction parameter (χFH). From the snapshots of the micellar structures and radial distribution function of polymer blocks, it is clearly presented that the micelle is multicompartmental. In addition, by implementing the DPD simulations in the presence of reactants, it is found that Reac-C4 and Reac-OPh are associate well with the hydrophilic shell of the micelle, whereas the other two reactants, Reac-Ph and Reac-Cl, are not incorporated into the micelle. From our DPD simulations, we confirm that the miscibility (solubility) of reactant with the micelle has a strong correlation with the rate of hydrolysis kinetic resolution. Utilizing accurate methods evaluating accurate χFH parameters for molecular interactions in micelle system, this DPD simulation can have a great potential to predict the structures of micelles consisting of designed multiblock copolymers for useful reactions.

Characterization of molecular association of poly(2-oxazoline)s-based micelles with various epoxides and diols via the Flory-Huggins theory: a molecular dynamics simulation approach.

The hydrolytic kinetic resolution (HKR) of epoxides has been performed in a shell-crosslinked micellar (SCM) nanoreactor consisting of amphiphilic triblock copolymers based on poly(2-oxazline)s polymer derivatives with attached Co(iii)-salens to the micelle core. To investigate the effect of the molecular interaction of reactant/product molecules with the SCM nanoreactor on the rate of HKR, we calculated the Flory-Huggins interaction parameters (χ) using the molecular dynamics simulation method. For this, the blend systems were constructed with various compositions such as 15, 45, and 70 wt% of the reactant/product molecules with respect to the polymers such as poly(2-methyl-2-oxazoline) (PMOX), poly(2-(3-butinyl)2-oxazoline) (PBOX), and poly(methyl-3-oxazol-2-yl)pentanoate with Co(iii)-salen (PSCoX). From the χ parameters, we demonstrate that the miscibility of reactants/products with polymers has a strong correlation with the experimental reaction rate of the HKR: phenyl glycidyl ether (Reac-OPh) > epoxyhexane (Reac-C4) > styrene oxide (Reac-Ph) > epichlorohydrin (Reac-Cl). To validate this finding, we also conducted the potential of mean force analysis using steered molecular dynamics simulation for the molecular displacement of Reac-Cl and Reac-OPh through PMOX and PSCoX, revealing that the free energy reduction was greater when Reac-OPh molecule enters the polymer phase compared to Reac-Cl, which agrees with the findings from the χ parameters calculations.

Monitoring of inflammation using novel biosensor mouse model reveals tissue- and sex-specific responses to Western diet.

Obesity is an epidemic, and it is characterized by a state of low-grade systemic inflammation. A key component of inflammation is the activation of inflammasomes, multiprotein complexes that form in response to danger signals and that lead to activation of caspase-1. Previous studies have found that a Westernized diet induces activation of inflammasomes and production of inflammatory cytokines. Gut microbiota metabolites, including the short-chain fatty acid butyrate, have received increased attention as underlying some obesogenic features, but the mechanisms of action by which butyrate influences inflammation in obesity remain unclear. We engineered a caspase-1 reporter mouse model to measure spatiotemporal dynamics of inflammation in obese mice. Concurrent with increased capsase-1 activation in vivo, we detected stronger biosensor signal in white adipose and heart tissues of obese mice ex vivo and observed that a short-term butyrate treatment affected some, but not all, of the inflammatory responses induced by Western diet. Through characterization of inflammatory responses and computational analyses, we identified tissue- and sex-specific caspase-1 activation patterns and inflammatory phenotypes in obese mice, offering new mechanistic insights underlying the dynamics of inflammation.

Outer membrane protein size and LPS O-antigen define protective antibody targeting to the Salmonella surface.

Lipopolysaccharide (LPS) O-antigen (O-Ag) is known to limit antibody binding to surface antigens, although the relationship between antibody, O-Ag and other outer-membrane antigens is poorly understood. Here we report, immunization with the trimeric porin OmpD from Salmonella Typhimurium (STmOmpD) protects against infection. Atomistic molecular dynamics simulations indicate this is because OmpD trimers generate footprints within the O-Ag layer sufficiently sized for a single IgG Fab to access. While STmOmpD differs from its orthologue in S. Enteritidis (SEn) by a single amino-acid residue, immunization with STmOmpD confers minimal protection to SEn. This is due to the OmpD-O-Ag interplay restricting IgG binding, with the pairing of OmpD with its native O-Ag being essential for optimal protection after immunization. Thus, both the chemical and physical structure of O-Ag are key for the presentation of specific epitopes within proteinaceous surface-antigens. This enhances combinatorial antigenic diversity in Gram-negative bacteria, while reducing associated fitness costs.