How macromolecules softness affects diffusion under crowding

Słyk, Edyta; Skóra, Tomasz; Kondrat, Svyatoslav

doi:10.1039/d2sm00357k

Cited by 10 publications

(15 citation statements)

References 52 publications

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“…The Brownian motion observed in unentangled PEGDA in this work, as reflected by a β̅ value ranging from 0.87 to 1.12 (depending on the particle size), is in good agreement with the previous results and moreover suggests that the chain entanglement is likely due to be the major cause for the particle diffusion over micrometer length scales to become subdiffusive on the time scale of the measurement. These experimental findings are in good agreement to theoretical simulation works. , The wide distribution of our β values seen here are more likely related to the local fluctuations in the nanoparticles’ diffusion dynamics than the real subdiffusive ,,, or hyperdiffusive , behaviors, as previously reported. It should be noted that tMSD analysis alone does not provide a full picture on the transport mode in complex polymer solutions.…”

Section: Resultssupporting

confidence: 93%

“…These experimental findings are in good agreement to theoretical simulation works. 79,80 The wide distribution of our β values seen here are more likely related to the local fluctuations in the nanoparticles' diffusion dynamics than the real subdiffusive 43,46,63,68 or hyperdiffusive 100,101 behaviors, as previously reported. It should be noted that tMSD analysis alone does not provide a full picture on the transport mode in complex polymer solutions.…”

Section: ■ Results and Discussionsupporting

confidence: 69%

“…In a subsequent Brownian dynamic simulation by the same group, the effect of the softness of molecular crowders on the tracer diffusion was studied to reveal that harder crowding molecules are more effective in slowing down the diffusion of spherical tracers . Interestingly, the diffusion of elongated tracer molecules, such as double-stranded DNA, were not significantly impacted by the softness of the crowders …”

Section: Introductionmentioning

confidence: 99%

“…76 The softness and shape of the tracer particles and crowding molecules could also impact the diffusion of tracers in a crowded media, as previously reported. 79,80 Skoŕa and coworkers observed a significant reduction in the streptavidin tracer mobility when the shape of the macromolecular crowders are cylindrical (double-stranded DNA) rather than spherical (Ficoll 70). 80 In a subsequent Brownian dynamic simulation by the same group, the effect of the softness of molecular crowders on the tracer diffusion was studied to reveal that harder crowding molecules are more effective in slowing down the diffusion of spherical tracers.…”

Section: ■ Introductionmentioning

confidence: 99%

“…79 Interestingly, the diffusion of elongated tracer molecules, such as double-stranded DNA, were not significantly impacted by the softness of the crowders. 79 In this study, we systematically studied the diffusion behaviors of individual probe particles in unentangled PEGDA solutions as a function of their size using SPT. A short chain PEGDA (M n = 700 g mol −1 ) was used to form unentangled polymer matrices in the semidilute regime.…”

Section: ■ Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Single-Particle Tracking in Poly(Ethylene Glycol) Diacrylate: Probe Size Effect on the Diffusion Behaviors of Nanoparticles in Unentangled Polymer Solutions

Foreman,

Tran-Ba

2023

J. Phys. Chem. B

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A thorough understanding of the relevant factors governing the transport of nanoparticles in poly(ethylene glycol) diacrylate (PEGDA) is crucial for many applications utilizing this polymer. Here, single-particle tracking (SPT) was used to systematically investigate the role of the probe size (3−200 nm) on the diffusion behaviors of individual fluorescent nanoparticles in semidilute and unentangled PEGDA solutions. The quantitative assessment of the SPT data via the recorded single-particle trajectories and diffusion coefficients (D) not only showed that the observed probe dynamics in PEGDA were temporally and spatially heterogeneous, but more importantly that the measured D were observed to be significantly reduced (vs in solvent) and strongly size-dependent. We explained these results based on a modified multiscale model for particle diffusion, built upon wellestablished hydrodynamics and obstruction theories. We furthermore showed that the presence of steric interactions and probe confinement effects in highly crowded, unentangled PEGDA microstructures can lead to deviations in the single-particle displacements from the expected Gaussian behavior, as revealed by the van Hove displacement distributions and the associated non-Gaussian parameters. This study has demonstrated the power of SPT methods in offering an advanced characterization of the transport characteristics in complex polymer structures, overcoming challenges posed by traditional characterization techniques.

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Section: Resultssupporting

confidence: 93%

Section: ■ Results and Discussionsupporting

confidence: 69%

Section: Introductionmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Single-Particle Tracking in Poly(Ethylene Glycol) Diacrylate: Probe Size Effect on the Diffusion Behaviors of Nanoparticles in Unentangled Polymer Solutions

Foreman,

Tran-Ba

2023

J. Phys. Chem. B

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Minimal Coarse-Grained Model for Immunoglobulin G: Diffusion and Binding under Crowding

Słyk,

Skóra,

Kondrat

2023

J. Phys. Chem. B

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Immunoglobulin G (IgG) is the most common type of antibody found in blood and extracellular fluids and plays an essential role in our immune response. However, studies of the dynamics and reaction kinetics of IgG–antigen binding under physiological crowding conditions are scarce. Herein, we develop a coarse-grained model of IgG consisting of only six beads that we find minimal for a coarse representation of IgG’s shape and a decent reproduction of its flexibility and diffusion properties measured experimentally. Using this model in Brownian dynamics simulations, we find that macromolecular crowding affects only slightly the IgG’s flexibility, as described by the distribution of angles between the IgG’s arms and stem. Our simulations indicate that, contrary to expectations, crowders slow down the translational diffusion of an IgG less strongly than they do for a smaller Ficoll 70, which we relate to the IgG’s conformational size changes induced by crowding. We also find that crowders affect the binding kinetics by decreasing the rate of the first binding step and enhancing the second binding step.

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Size Sensitivity of Metabolite Diffusion in Macromolecular Crowds

Raczyłło,

Gołowicz,

Skóra

et al. 2024

Nano Lett.

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Metabolites play crucial roles in cellular processes, yet their diffusion in the densely packed interiors of cells remains poorly understood, compounded by conflicting reports in existing studies. Here, we employ pulsed-gradient stimulated-echo NMR and Brownian/Stokesian dynamics simulations to elucidate the behavior of nano-and subnanometer-sized tracers in crowded environments. Using Ficoll as a crowder, we observe a linear decrease in tracer diffusivity with increasing occupied volume fraction, persisting�somewhat surprisingly�up to volume fractions of 30−40%. While simulations suggest a linear correlation between diffusivity slowdown and particle size, experimental findings hint at a more intricate relationship, possibly influenced by Ficoll's porosity. Simulations and numerical calculations of tracer diffusivity in the E. coli cytoplasm show a nonlinear yet monotonic diffusion slowdown with particle size. We discuss our results in the context of nanoviscosity and discrepancies with existing studies.

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How macromolecules softness affects diffusion under crowding

Abstract: Diffusion in a macromolecularly crowded environment is essential for many intracellular processes, from metabolism and catalysis to gene transcription and translation. So far, theoretical and experimental work has focused on...

Cited by 10 publications

References 52 publications

Single-Particle Tracking in Poly(Ethylene Glycol) Diacrylate: Probe Size Effect on the Diffusion Behaviors of Nanoparticles in Unentangled Polymer Solutions

Single-Particle Tracking in Poly(Ethylene Glycol) Diacrylate: Probe Size Effect on the Diffusion Behaviors of Nanoparticles in Unentangled Polymer Solutions

Minimal Coarse-Grained Model for Immunoglobulin G: Diffusion and Binding under Crowding

Size Sensitivity of Metabolite Diffusion in Macromolecular Crowds

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