Adsorption of Lysozyme Into a Charged Confining Pore

Caetano, Daniel L. Z.; Metzler, Ralf; Cherstvy, Andrey G.; Carvalho, Sidney J. de

doi:10.1101/2021.07.11.451934

Cited by 3 publications

(3 citation statements)

References 82 publications

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“…Although an elastic dimer can be considered as a model of shape-asymmetric proteins 132,199 , 3D computer simulations with electrostatic interactions and hydrodynamic effects 63 -instead of 2D simulations without these two effects-are required to approach the problem of macromolecular crowding as realized in many biological cells. Crowding by shape-elongated molecules can have implications onto the properties of biomolecular reactions 66 (including protein folding and protein-protein association) as well as of polymer and DNA looping.…”

Section: B Physical Rationales and Further Discussionmentioning

confidence: 99%

Non-Gaussian, transiently anomalous, and ergodic self-diffusion of flexible dumbbells in crowded two-dimensional environments: Coupled translational and rotational motions

et al. 2021

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We employ Langevin-dynamics simulations to unveil non-Brownian and non-Gaussian center-ofmass self-diffusion of massive flexible dumbbell-shaped particles in crowded two-dimensional solutions. We also study the intra-dumbbell dynamics due to the relative motion of the two constituent elastically-coupled disks. Our main focus is on effects of the crowding fraction φ and the particle structure on the diffusion characteristics. We evaluate the time-averaged mean-squared displacement (TAMSD), the displacement probability-density function (PDF) and the displacement autocorrelation function (ACF) of the dimers. For the TAMSD at highly crowded conditions of dumbbells, e.g., we observe a transition from the short-time ballistic behavior, via an intermediate subdiffusive regime, to long-time Brownian-like spreading dynamics. The crowded system of dimers exhibits two distinct diffusion regimes distinguished by the scaling exponent of the TAMSD, the dependence of the diffusivity on φ, and the features of the displacement-ACF. We attribute these regimes to a crowding-induced transition from a viscous to a viscoelastic diffusion medium upon growing φ. We also analyze the relative motion in the dimers, finding that larger φ suppress their vibrations and yield strongly non-Gaussian PDFs of rotational displacements. For the diffusion coefficients D(φ) of translational and rotational motion of the dumbbells an exponential decay with φ for weak and a power-law D(φ) ∝ (φ − φ ) 2.4 for strong crowding is found. A comparison of simulation results with theoretical predictions for D(φ) is discussed and some relevant experimental systems are overviewed.

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Section: B Physical Rationales and Further Discussionmentioning

confidence: 99%

Non-Gaussian, transiently anomalous, and ergodic self-diffusion of flexible dumbbells in crowded two-dimensional environments: Coupled translational and rotational motions

et al. 2021

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“…In a more recent work, coarse grain MD and constant-pH Monte Carlo (MC) simulations were used to study the lysozyme adsorption on negatively charged SNPs. The results showed that the increase of pH leads to changes in orientation of the adsorbed lysozyme when the solution pH gets closer to the enzyme's isoelectric point (Caetano et al, 2021). MD simulations were also used by Wang et al (2020) to tune the immobilization of a lipase on SNPs.…”

Section: Immobilization On Nanoparticlesmentioning

confidence: 99%

Enzyme immobilization studied through molecular dynamic simulations

Bhattacharjee¹,

Alonso‐Cotchico²,

Lucas³

2023

Front. Bioeng. Biotechnol.

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In recent years, simulations have been used to great advantage to understand the structural and dynamic aspects of distinct enzyme immobilization strategies, as experimental techniques have limitations in establishing their impact at the molecular level. In this review, we discuss how molecular dynamic simulations have been employed to characterize the surface phenomenon in the enzyme immobilization procedure, in an attempt to decipher its impact on the enzyme features, such as activity and stability. In particular, computational studies on the immobilization of enzymes using i) nanoparticles, ii) self-assembled monolayers, iii) graphene and carbon nanotubes, and iv) other surfaces are covered. Importantly, this thorough literature survey reveals that, while simulations have been primarily performed to rationalize the molecular aspects of the immobilization event, their use to predict adequate protocols that can control its impact on the enzyme properties is, up to date, mostly missing.

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“…We note that a recent Monte Carlo simulation study investigated the selective adsorption of lysozyme confined within a charged cylindrical surface, 37 where the lysozyme behaves as a polyampholyte depending on the pH of the solution. It was found that the charge patches and the charge regulation processes are critical to the lysozyme adsorption.…”

Section: Resultsmentioning

confidence: 99%

Selective Adsorption of Confined Polymers: Self-Consistent Field Theory Studies

2021

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Selective adsorption of flexible polymers, where only a fraction of the "sticker" monomers can be adsorbed, confined to a cylindrical pore, is studied within the self-consistent field theory (SCFT). The selective adsorption, modeled with diblock, alternating, and random distributions of the sticker monomers along the chain, shows different adsorption−desorption transition behaviors: when the polymer chain possesses a high fraction of stickers, the di-block sequence adsorbs better than the alternating and the random sequence. On the other hand, when the polymer chain possesses a low fraction of stickers, the alternating sequence is the most adsorbed chain. Our theory indicates that the correlation between stickers and nonadsorbing monomers (neutrals) enhances the adsorption of polymers at a low fraction of sticker monomers, while it hinders the adsorption of polymers at a high fraction of sticker monomers, revealing the mechanism of adsorption efficiency determined by the sequence of sticker monomers in a polymer chain.

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Adsorption of Lysozyme Into a Charged Confining Pore

Cited by 3 publications

References 82 publications

Non-Gaussian, transiently anomalous, and ergodic self-diffusion of flexible dumbbells in crowded two-dimensional environments: Coupled translational and rotational motions

Non-Gaussian, transiently anomalous, and ergodic self-diffusion of flexible dumbbells in crowded two-dimensional environments: Coupled translational and rotational motions

Enzyme immobilization studied through molecular dynamic simulations

Selective Adsorption of Confined Polymers: Self-Consistent Field Theory Studies

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