The effect of composition on diffusion of macromolecules in a crowded environment

Kondrat, Svyatoslav; Zimmermann, Olav; Wiechert, Wolfgang; Lieres, Eric von

doi:10.1088/1478-3975/12/4/046003

Cited by 37 publications

(44 citation statements)

References 50 publications

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“…There, the crowding induced changes in the diffusion of signalling molecules is expected to impact gene regulation and metabolism [127] and also alter active transport properties [21,33,34,128]. Other extensions of the current model include polydisperse static and dynamic crowders [129][130][131], cylindrical domains mimicking a typical bacterial shape [55,132], specific and non-specific tracer-crowder interactions [55,61], three-dimensional computer simulations, a variable tracer size, as well as deformable and non-spherical crowding particles [133,134].…”

Section: Discussionmentioning

confidence: 99%

Anomalous, non-Gaussian tracer diffusion in crowded two-dimensional environments

et al. 2016

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A topic of intense current investigation pursues the question of how the highly crowded environment of biological cells affects the dynamic properties of passively diffusing particles. Motivated by recent experiments we report results of extensive simulations of the motion of a finite sized tracer particle in a heterogeneously crowded environment made up of quenched distributions of monodisperse crowders of varying sizes in finite circular two-dimensional domains. For given spatial distributions of monodisperse crowders we demonstrate how anomalous diffusion with strongly non-Gaussian features arises in this model system. We investigate both biologically relevant situations of particles released either at the surface of an inner domain or at the outer boundary, exhibiting distinctly different features of the observed anomalous diffusion for heterogeneous distributions of crowders. Specifically we reveal an asymmetric spreading of tracers even at moderate crowding. In addition to the mean squared displacement (MSD) and local diffusion exponent we investigate the magnitude and the amplitude scatter of the time averaged MSD of individual tracer trajectories, the non-Gaussianity parameter, and the van Hove correlation function. We also quantify how the average tracer diffusivity varies with the position in the domain with a heterogeneous radial distribution of crowders and examine the behaviour of the survival probability and the dynamics of the tracer survival probability. Inter alia, the systems we investigate are related to the passive transport of lipid molecules and proteins in two-dimensional crowded membranes or the motion in colloidal solutions or emulsions in effectively two-dimensional geometries, as well as inside supercrowded, surface adhered cells.

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Section: Discussionmentioning

confidence: 99%

Anomalous, non-Gaussian tracer diffusion in crowded two-dimensional environments

et al. 2016

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“…122 Anomalous diffusion results in diffusion rates varying on different time scales due to confinement within cellular compartments and caging effects due to temporary encapsulation by larger crowders. 34,123,125−128 However, details of how diffusion is modulated by different cellular microenvironments and by the presence of DNA or membrane surfaces have remained unclear. 77 There is also an incomplete understanding of how smaller molecules, metabolites and other ligands navigate the dense cellular environments where available space is not just limited and solvent viscosity may be altered but where the various macromolecular surfaces also provide ample opportunities for distractions that could, for example, slow down diffusion toward an enzyme active site.…”

Section: Key Questionsmentioning

confidence: 99%

“…6,13−15 At the same time, increasing attention is now focused on the effects of interactions between the cellular components 16−24 and altered solvent properties, 25−30 often contributing enthalpically, 15,31,32 as well as the consequences of a substantial compositional heterogeneity present in biological cells. 33,34 …”

Section: Introductionmentioning

confidence: 99%

Crowding in Cellular Environments at an Atomistic Level from Computer Simulations

et al. 2017

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The effects of crowding in biological environments on biomolecular structure, dynamics, and function remain not well understood. Computer simulations of atomistic models of concentrated peptide and protein systems at different levels of complexity are beginning to provide new insights. Crowding, weak interactions with other macromolecules and metabolites, and altered solvent properties within cellular environments appear to remodel the energy landscape of peptides and proteins in significant ways including the possibility of native state destabilization. Crowding is also seen to affect dynamic properties, both conformational dynamics and diffusional properties of macromolecules. Recent simulations that address these questions are reviewed here and discussed in the context of relevant experiments.

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“…One important topic is how crowding affects protein diffusion, which has been investigated using Brownian dynamics, with hydrodynamic interactions described in different ways [45][46][47][48]. These studies focus on rigid-body motions.…”

Section: Scopementioning

confidence: 99%

Protein folding/unfolding in the presence of interacting macromolecular crowders

Irbäck

Mohanty

2017

Eur. Phys. J. Spec. Top.

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Abstract. Recent years have seen an increasing number of biophysical studies of proteins being conducted in cells and concentrated protein solutions. In these experiments, compared to dilute-solution data, both stabilization and destabilization of globular proteins have been observed, which cannot be explained in terms of volume exclusion alone. For a fundamental understanding of the observed effects, there is a need for computational modeling beyond the level of hard-sphere crowders. This mini-review discusses recent efforts to simulate folding/unfolding properties of proteins in the presence of explicit macromolecular crowders. A Monte Carlo-based approach by us is described, which we recently applied to study the equilibrium folding thermodynamics of two peptides in the presence of explicit protein crowders.

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The effect of composition on diffusion of macromolecules in a crowded environment

Cited by 37 publications

References 50 publications

Anomalous, non-Gaussian tracer diffusion in crowded two-dimensional environments

Anomalous, non-Gaussian tracer diffusion in crowded two-dimensional environments

Crowding in Cellular Environments at an Atomistic Level from Computer Simulations

Protein folding/unfolding in the presence of interacting macromolecular crowders

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