Co-localization and confinement of ecto-nucleotidases modulate extracellular adenosine nucleotide distributions

Purinoreceptors and ectonucleotidases control ATP-induced calcium waveforms and calcium-dependent responses in microglia: Roles of P2 receptors and CD39 in ATP-stimulated microglia

Adenosine triphosphate (ATP) and its metabolites drive microglia migration and cytokine production by activating P2X- and P2Y- class purinergic receptors. Purinergic receptor activation gives rise to diverse intracellular calcium (Ca2+ signals, or waveforms, that differ in amplitude, duration, and frequency. Whether and how these characteristics of diverse waveforms influence microglia function is not well-established. We developed a computational model trained with data from published primary murine microglia studies. We simulate how purinoreceptors influence Ca2+ signaling and migration, as well as, how purinoreceptor expression modifies these processes. Our simulation confirmed that P2 receptors encode the amplitude and duration of the ATP-induced Ca2+ waveforms. Our simulations also implicate CD39, an ectonucleotidase that rapidly degrades ATP, as a regulator of purinergic receptor-induced Ca2+ responses. Namely, it was necessary to account for CD39 metabolism of ATP to align the model's predicted purinoreceptor responses with published experimental data. In addition, our modeling results indicate that small Ca2+ transients accompany migration, while large and sustained transients are needed for cytokine responses. Lastly, as a proof-of-principal, we predict Ca2+ transients and cell membrane displacements in a BV2 microglia cell line using published P2 receptor mRNA data to illustrate how our computer model may be extrapolated to other microglia subtypes. These findings provide important insights into how differences in purinergic receptor expression influence microglial responses to ATP.

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.

Homogenization of Continuum-Scale Transport Properties from Molecular Dynamics Simulations: An Application to Aqueous-Phase Methane Diffusion in Silicate Channels

Silica-based materials including zeolites are commonly used for wide-ranging applications including separations and catalysis. Substrate transport rates in these materials can significantly influence the efficiency of such applications. Two factors that contribute to transport rates include (1) the porosity of the silicate matrix and (2) nonbonding interactions between the diffusing species and the silicate surface. These contributions generally emerge from disparate length scales, namely, "microscopic" (roughly nanometer-scale) and "macroscopic" (roughly micron-scale), respectively. Here, we develop a simulation framework to estimate the simultaneous impact of these factors on methane mass transport in silicate channels. Specifically, we develop a model of methane transport using homogenization theory to obtain transport parameters valid at length scales of hundreds to thousands of nanometers. These parameters implicitly reflect interactions taking place at fractions of a nanometer. The inputs to the homogenization analysis are data from extensive molecular dynamics simulations that incorporate atomistic-scale interactions, processed to yield local diffusion coefficients and mean force potentials. With this model, we demonstrate how nuances in silicate hydration and silica/methane interactions impact methane diffusion rates in silicate materials, including the effects of silicate surface chemistry such as the presence of silanol groups. The molecular dynamics simulations indicate that methane diffusivity at the silica surface is lower than the bulk-like rates observed at the center of channels of sufficient width. However, potentials of mean force generally evidence attractive methane/silica interactions that enhance diffusion overall. By simultaneously accounting for both of these effects, we show that the effective diffusion coefficient for the nanoporous silicate can be approximately double the value of estimates assuming fully bulk-like behavior in the channel. This study therefore demonstrates the importance of determining diffusion coefficients and potentials of mean force at an atomistic level when estimating transport properties in bulk materials. Importantly, we provide a simple homogenization framework to incorporate these molecular-scale attributes into bulk material transport estimates. This hybrid homogenization/molecular dynamics approach will be of general use for describing small-molecule transport in materials with detailed molecular interactions.

Mechanical Principles Governing the Shapes of Dendritic Spines

Dendritic spines are small, bulbous protrusions along the dendrites of neurons and are sites of excitatory postsynaptic activity. The morphology of spines has been implicated in their function in synaptic plasticity and their shapes have been well-characterized, but the potential mechanics underlying their shape development and maintenance have not yet been fully understood. In this work, we explore the mechanical principles that could underlie specific shapes using a minimal biophysical model of membrane-actin interactions. Using this model, we first identify the possible force regimes that give rise to the classic spine shapes-stubby, filopodia, thin, and mushroom-shaped spines. We also use this model to investigate how the spine neck might be stabilized using periodic rings of actin or associated proteins. Finally, we use this model to predict that the cooperation between force generation and ring structures can regulate the energy landscape of spine shapes across a wide range of tensions. Thus, our study provides insights into how mechanical aspects of actin-mediated force generation and tension can play critical roles in spine shape maintenance.

Molecular Mechanics Study of Flow and Surface Influence in Ligand-Protein Association

Ligand–protein association is the first and critical step for many biological and chemical processes. This study investigated the molecular association processes under different environments. In biology, cells have different compartments where ligand–protein binding may occur on a membrane. In experiments involving ligand–protein binding, such as the surface plasmon resonance and continuous flow biosynthesis, a substrate flow and surface are required in experimental settings. As compared with a simple binding condition, which includes only the ligand, protein, and solvent, the association rate and processes may be affected by additional ligand transporting forces and other intermolecular interactions between the ligand and environmental objects. We evaluated these environmental factors by using a ligand xk263 binding to HIV protease (HIVp) with atomistic details. Using Brownian dynamics simulations, we modeled xk263 and HIVp association time and probability when a system has xk263 diffusion flux and a non-polar self-assembled monolayer surface. We also examined different protein orientations and accessible surfaces for xk263. To allow xk263 to access to the dimer interface of immobilized HIVp, we simulated the system by placing the protein 20Å above the surface because immobilizing HIVp on a surface prevented xk263 from contacting with the interface. The non-specific interactions increased the binding probability while the association time remained unchanged. When the xk263 diffusion flux increased, the effective xk263 concentration around HIVp, xk263–HIVp association time and binding probability decreased non-linearly regardless of interacting with the self-assembled monolayer surface or not. The work sheds light on the effects of the solvent flow and surface environment on ligand–protein associations and provides a perspective on experimental design.

Adenosine metabolism in the vascular system

The concept of extracellular purinergic signaling was first proposed by Geoffrey Burnstock in the early 1970s. Since then, extracellular ATP and its metabolites ADP and adenosine have attracted an enormous amount of attention in terms of their involvement in a wide range of immunomodulatory, thromboregulatory, angiogenic, vasoactive and other pathophysiological activities in different organs and tissues, including the vascular system. In addition to significant progress in understanding the properties of nucleotide- and adenosine-selective receptors, recent studies have begun to uncover the complexity of regulatory mechanisms governing the duration and magnitude of the purinergic signaling cascade. This knowledge has led to the development of new paradigms in understanding the entire purinome by taking into account the multitude of signaling and metabolic pathways involved in biological effects of ATP and adenosine and compartmentalization of the adenosine system. Along with the "canonical route" of ATP breakdown to adenosine via sequential ecto-nucleoside triphosphate diphosphohydrolase-1 (NTPDase1/CD39) and ecto-5'-nucleotidase/CD73 activities, it has now become clear that purine metabolism is the result of concerted effort between ATP release, its metabolism through redundant nucleotide-inactivating and counteracting ATP-regenerating ectoenzymatic pathways, as well as cellular nucleoside uptake and phosphorylation of adenosine to ATP through complex phosphotransfer reactions. In this review I provide an overview of key enzymes involved in adenosine metabolic network, with special emphasis on the emerging roles of purine-converting ectoenzymes as novel targets for cancer and vascular therapies.