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Journal of the American Chemical Society Mar 2022Recent studies have sparked debate over whether catalytic reactions enhance the diffusion coefficients of enzymes. Through high statistics of the transient (600 μs)...
Recent studies have sparked debate over whether catalytic reactions enhance the diffusion coefficients of enzymes. Through high statistics of the transient (600 μs) displacements of unhindered single molecules freely diffusing in common buffers, we here quantify for four enzymes under catalytic turnovers. We thus formulate how ∼ ±1% precisions may be achieved for , and show no changes in diffusivity for catalase, urease, aldolase, and alkaline phosphatase under the application of wide concentration ranges of substrates. Our single-molecule approach thus overcomes potential limitations and artifacts underscored by recent studies to show no enhanced diffusion in enzymatic reactions.
Topics: Alkaline Phosphatase; Diffusion; Fructose-Bisphosphate Aldolase; Nanotechnology; Urease
PubMed: 35258969
DOI: 10.1021/jacs.1c12328 -
Annual Review of Physiology 1987Membrane protein lateral diffusion can be constrained in several ways: Diffusion can be slower than that predicted for a simple, fluid lipid bilayer; diffusion can be... (Review)
Review
Membrane protein lateral diffusion can be constrained in several ways: Diffusion can be slower than that predicted for a simple, fluid lipid bilayer; diffusion can be confined to certain regions within the total membrane; and diffusion may not be equally probable in all directions, i.e. it may be anisotropic. We know that protein diffusion is reduced by increasing concentrations of membrane proteins and by interactions of the diffusant with structure(s) peripheral to the membrane. The molecular nature of such peripheral constraints has been difficult to pinpoint, but attention is now being directed to the extracellular matrix in addition to the membrane-associated cytoskeleton. There are many proteins that are confined to lateral domains in differentiated, isolated cells and in cells organized into tissue. The mechanisms that maintain such inhomogeneous distributions should be elucidated in the next few years. Whether lateral diffusion of membrane proteins over distances of a few micrometers is usually isotropic or anisotropic will be ascertained in the near future using imaging methods combined with photobleaching.
Topics: Diffusion; Lipid Bilayers; Membrane Proteins; Membranes
PubMed: 3551795
DOI: 10.1146/annurev.ph.49.030187.001115 -
Nature Methods Jun 2022Label-free characterization of single biomolecules aims to complement fluorescence microscopy in situations where labeling compromises data interpretation, is...
Label-free characterization of single biomolecules aims to complement fluorescence microscopy in situations where labeling compromises data interpretation, is technically challenging or even impossible. However, existing methods require the investigated species to bind to a surface to be visible, thereby leaving a large fraction of analytes undetected. Here, we present nanofluidic scattering microscopy (NSM), which overcomes these limitations by enabling label-free, real-time imaging of single biomolecules diffusing inside a nanofluidic channel. NSM facilitates accurate determination of molecular weight from the measured optical contrast and of the hydrodynamic radius from the measured diffusivity, from which information about the conformational state can be inferred. Furthermore, we demonstrate its applicability to the analysis of a complex biofluid, using conditioned cell culture medium containing extracellular vesicles as an example. We foresee the application of NSM to monitor conformational changes, aggregation and interactions of single biomolecules, and to analyze single-cell secretomes.
Topics: Diffusion; Microscopy, Fluorescence; Nanoparticles; Nanotechnology
PubMed: 35637303
DOI: 10.1038/s41592-022-01491-6 -
Journal of Chromatography. A May 2004Enhanced fluidity (EF) liquid mixtures are advantageous as mobile phases for the separation of moderate to polar compounds in liquid chromatography (reversed-phase,... (Review)
Review
Enhanced fluidity (EF) liquid mixtures are advantageous as mobile phases for the separation of moderate to polar compounds in liquid chromatography (reversed-phase, normal, size exclusion, size exclusion, and chiral separations). The low viscosities and high diffusivities of EF mixtures allow highly efficient separations to be achieved in a small amount of time. The best use of enhanced-fluidity liquids is only possible when their physicochemical properties are known. Herein, the techniques used to measure the physicochemical properties (phase diagram, diffusivity, solvent strength and pH) of EF liquids are described. For each technique, the experiment design and the care necessary to insure the quality of the collected data are described. Finally, the impact of the measured physicochemical properties on the chromatography is also highlighted.
Topics: Chemical Phenomena; Chemistry, Physical; Diffusion; Hydrogen-Ion Concentration; Solutions; Solvents
PubMed: 15214678
DOI: 10.1016/j.chroma.2004.04.001 -
Single-molecule displacement mapping unveils nanoscale heterogeneities in intracellular diffusivity.Nature Methods May 2020Intracellular diffusion underlies vital cellular processes. However, it remains difficult to elucidate how an unbound protein diffuses inside the cell with good spatial...
Intracellular diffusion underlies vital cellular processes. However, it remains difficult to elucidate how an unbound protein diffuses inside the cell with good spatial resolution and sensitivity. Here we introduce single-molecule displacement/diffusivity mapping (SMdM), a super-resolution strategy that enables the nanoscale mapping of intracellular diffusivity through local statistics of the instantaneous displacements of freely diffusing single molecules. We thus show that the diffusion of an average-sized protein in the mammalian cytoplasm and nucleus is spatially heterogeneous at the nanoscale, and that variations in local diffusivity correlate with the ultrastructure of the actin cytoskeleton and the organization of the genome, respectively. SMdM of differently charged proteins further unveils that the possession of positive, but not negative, net charges drastically impedes diffusion, and that the rate is determined by the specific subcellular environments. We thus unveil rich heterogeneities and charge effects in intracellular diffusion at the nanoscale.
Topics: Cell Nucleus; Cells, Cultured; Cytoplasm; Diffusion; Humans; Image Interpretation, Computer-Assisted; Intracellular Space; Microscopy, Fluorescence; Models, Theoretical; Nanoparticles; Proteins; Single Molecule Imaging
PubMed: 32203387
DOI: 10.1038/s41592-020-0793-0 -
Journal of the Royal Society, Interface Jul 2023Turing's mechanism is often invoked to explain periodic patterns in nature, although direct experimental support is scarce. Turing patterns form in reaction-diffusion...
Turing's mechanism is often invoked to explain periodic patterns in nature, although direct experimental support is scarce. Turing patterns form in reaction-diffusion systems when the activating species diffuse much slower than the inhibiting species, and the involved reactions are highly nonlinear. Such reactions can originate from cooperativity, whose physical interactions should also affect diffusion. We here take direct interactions into account and show that they strongly affect Turing patterns. We find that weak repulsion between the activator and inhibitor can substantially lower the required differential diffusivity and reaction nonlinearity. By contrast, strong interactions can induce phase separation, but the resulting length scale is still typically governed by the fundamental reaction-diffusion length scale. Taken together, our theory connects traditional Turing patterns with chemically active phase separation, thus describing a wider range of systems. Moreover, we demonstrate that even weak interactions affect patterns substantially, so they should be incorporated when modelling realistic systems.
Topics: Diffusion
PubMed: 37434500
DOI: 10.1098/rsif.2023.0244 -
The Journal of Physical Chemistry. B May 2022Compared with univalent cationic diffusion, little is known about the diffusion behavior of multivalent cations let alone the diffusion of water in their first hydration...
Compared with univalent cationic diffusion, little is known about the diffusion behavior of multivalent cations let alone the diffusion of water in their first hydration shell. Here, we show that all published translational diffusion coefficients of multivalent cations and water measured at room temperature exhibit the same concentration dependence when plotted as a function of the mass fraction of free water or of hydrated solute. This behavior is held until only hydration and confined water remain in solutions, wherein their concentration dependences become cationic charge number-dependent. We also found that the iceberg model can well describe the diffusions of multivalent cations with decreasing water content until only hydration water is present. However, H-pulsed-field-gradient nuclear magnetic resonance measurements confirmed that H in the first hydration shell diffuses faster than Al at room temperature and they have the same diffusion coefficient only with decreasing the temperature down to about 243 K. Therefore, iceberg model only equivalently describes the effect of strong ion-water interaction on multivalent cationic diffusion. These results will also help us reconceive our current understanding of the pathway for hydration water affecting the diffusion behavior of solutes with relatively weak solute-water interactions.
Topics: Cations; Diffusion; Solutions; Temperature; Water
PubMed: 35543216
DOI: 10.1021/acs.jpcb.2c02110 -
International Journal of Pharmaceutics Oct 2011Mathematical models for the release of drug from both non-degradable and degradable slab matrices in which the initial drug loading is greater than the solubility are... (Review)
Review
Mathematical models for the release of drug from both non-degradable and degradable slab matrices in which the initial drug loading is greater than the solubility are presented in this paper. Taking the anomalous diffusions in the drug release processes into account, the fractional calculus is introduced to model the related phenomena. To describe different kinds of anomalous diffusions, corresponding fractional diffusion equations are adopted. By employing the integral transform methods, similarity solution method and perturbation method, exact and approximation solutions to the models are obtained.
Topics: Delayed-Action Preparations; Diffusion; Mathematics; Models, Theoretical; Solubility
PubMed: 21163340
DOI: 10.1016/j.ijpharm.2010.12.009 -
Biophysical Journal Oct 2021Erk signaling regulates cellular decisions in many biological contexts. Recently, we have reported a series of Erk activity traveling waves that coordinate regeneration...
Erk signaling regulates cellular decisions in many biological contexts. Recently, we have reported a series of Erk activity traveling waves that coordinate regeneration of osteoblast tissue in zebrafish scales. These waves originate from a central source region, propagate as expanding rings, and impart cell growth, thus controlling tissue morphogenesis. Here, we present a minimal reaction-diffusion model for Erk activity waves. The model considers three components: Erk, a diffusible Erk activator, and an Erk inhibitor. Erk stimulates both its activator and inhibitor, forming a positive and negative feedback loop, respectively. Our model shows that this system can be excitable and propagate Erk activity waves. Waves originate from a pulsatile source that is modeled by adding a localized basal production of the activator, which turns the source region from an excitable to an oscillatory state. As Erk activity periodically rises in the source, it can trigger an excitable wave that travels across the entire tissue. Analysis of the model finds that positive feedback controls the properties of the traveling wavefront and that negative feedback controls the duration of Erk activity peak and the period of Erk activity waves. The geometrical properties of the waves facilitate constraints on the effective diffusivity of the activator, indicating that waves are an efficient mechanism to transfer growth factor signaling rapidly across a large tissue.
Topics: Animals; Diffusion; Models, Theoretical; Osteoblasts; Signal Transduction; Zebrafish
PubMed: 34022234
DOI: 10.1016/j.bpj.2021.05.004 -
Soft Matter Oct 2023The lateral diffusion of cell membrane inclusions, such as integral membrane proteins and bound receptors, drives critical biological processes, including the formation...
The lateral diffusion of cell membrane inclusions, such as integral membrane proteins and bound receptors, drives critical biological processes, including the formation of complexes, cell-cell signaling, and membrane trafficking. These diffusive processes are complicated by how concentrated, or "crowded", the inclusions are, which can occupy between 30-50% of the area fraction of the membrane. In this work, we elucidate the effects of increasing concentration of model membrane inclusions in a free-standing artificial cell membrane on inclusion diffusivity and the apparent viscosity of the membrane. By multiple particle tracking of fluorescent microparticles covalently tethered to the bilayer, we show the transition from expected Brownian dynamics, which accurately measure the membrane viscosity, to subdiffusive behavior with decreased diffusion coefficient as the particle area fraction increases from 1% to around 30%, approaching physiological levels of crowding. At high crowding, the onset of non-Gaussian behavior is observed. Using hydrodynamic models relating the 2D diffusion coefficient to the viscosity of a membrane, we determine the apparent viscosity of the bilayer from the particle diffusivity and show an increase in the apparent membrane viscosity with increasing particle area fraction. However, the scaling of this increase is in contrast with the behavior of monolayer inclusion diffusion and bulk suspension rheology. These results demonstrate that physiological levels of model membrane crowding nontrivially alter the dynamics and apparent viscosity of the system, which has implications for understanding membrane protein interactions and particle-membrane transport processes.
Topics: Membranes; Membrane Proteins; Molecular Dynamics Simulation; Biophysical Phenomena; Diffusion; Membranes, Artificial; Viscosity
PubMed: 37791427
DOI: 10.1039/d3sm01269g