Enzyme localization, crowding, and buffers collectively modulate diffusion-influenced signal transduction: Insights from continuum diffusion modeling

Abstract

Biochemical reaction networks consisting of coupled enzymes connect substrate signaling events with biological function. Substrates involved in these reactions can be strongly influenced by diffusion "barriers" arising from impenetrable cellular structures and macromolecules, as well as interactions with biomolecules, especially within crowded environments. For diffusion-influenced reactions, the spatial organization of diffusion barriers arising from intracellular structures, non-specific crowders, and specific-binders (buffers) strongly controls the temporal and spatial reaction kinetics. In this study, we use two prototypical biochemical reactions, a Goodwin oscillator, and a reaction with a periodic source/sink term to examine how a diffusion barrier that partitions substrates controls reaction behavior. Namely, we examine how conditions representative of a densely packed cytosol, including reduced accessible volume fraction, non-specific interactions, and buffers, impede diffusion over nanometer length-scales. We find that diffusion barriers can modulate the frequencies and amplitudes of coupled diffusion-influenced reaction networks, as well as give rise to "compartments" of decoupled reactant populations. These effects appear to be intensified in the presence of buffers localized to the diffusion barrier. These findings have strong implications for the role of the cellular environment in tuning the dynamics of signaling pathways. C 2015 AIP Publishing LLC. [http://dx

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

“…These models provided strong quantitative insights into the efficiency of catalytic processes [45] and limits on efficiency gains for sequentially-coupled enzymes [46], but only implicitly account for geometrical and physiochemical factors. Explicit consideration of those factors for coupled enzyme processes generally involve partial differential equations or particle-based solutions, which have afforded descriptions of how neighboring reactive enzymes [47][48][49][50], feedback inhibition, [45,49], protein geometry and electrostatic interactions [23,25,51,52] contribute to enzyme activity, but have not been applied to NDA-dependent processes. We therefore extend these approaches by modeling in spatial detail the concerted hydrolysis of nucleotides by CD39 and CD73 nucleotidases.…”

Modeling somite scaling in small embryos in the framework of Turing patterns

“…Furthermore, physiological media are known to suffer from confinement [33,34,35,36,37,38] and we propose to address the issue of size adaptation in the general context of molecular crowding. We start from the intuitive statement that the effect of confinement is stronger in smaller embryos.…”

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

“…The thermodynamics and kinetics of molecular signaling in such compartments can differ considerably from analogous processes in bulk solutions or in vitro. Myriad factors contribute to these differences, including smaller compartment volumes that strongly amplify substrate concentration gradients [30, 72], the presence of ‘crowders’ comprising other small molecules, protein or nucleic acid that generally impede diffusion [28, 47, 73, 74], as well as rate enhancements typically exhibited for closely-apposed enzymes [29, 42, 45, 50, 75] or those adopting electrostatic fields complementary to a reacting species [38]. The relative contribution of these factors to coupled NDA activity in a given multi-cellular domain has not been examined previously and could ultimately determine the relative distribution of nucleotides.…”

“…For instance, nucleotides are generally negatively-charged and are thus attracted to positively-charged nucleotide binding sites of NDA[24]. Most notably, cellular ‘crowders’ comprising enzymes, proteins, and macromolecules typically reduce substrates’ intrinsic diffusion rates, which in turn can manifest in altered enzyme kinetics [23, 25–29]. Additionally, diffusion limitations stemming from densely packed media or impermeable membranes can confine substrates to narrow ‘microdomains’, within which substrate concentrations are vastly different from those in the bulk cytosol or extracellular medium [30].…”

“…These models provided strong quantitative insights into the efficiency of catalytic processes [46] and limits on efficiency gains for sequentially-coupled enzymes [45], but only implicitly account for geometrical and physiochemical factors. Explicit consideration of those factors for coupled enzyme processes generally utilize partial differential equations or particle-based solutions, which have afforded descriptions of how neighboring reactive enzymes [29, 47, 48], feedback inhibition, [29, 46], protein geometry and electrostatic interactions [19, 21, 49, 50] contribute to enzyme activity. Still, a systematic study of sequential reaction phenomena under physiological variations in solvent ionic strength and intracellular confinement is needed for probing how nucleotide pools are regulated by sequential NDAs in geometrically-constrained intercellular junctions.…”