Macromolecular crowding impacts on the diffusion and conformation of DNA hairpins

Nanoparticle transport in biomimetic polymer-linked emulsions

The ability of nanoparticles to penetrate and transport through soft tissues is essential to delivering therapeutics to treat diseases or signaling agents for advanced imaging and sensing. Nanoparticle transport in biological systems, however, is challenging to predict and control due to the physicochemical complexity of tissues and biological fluids. Here, we demonstrate that nanoparticles suspended in a novel class of soft matter-polymer-linked emulsions (PLEs)-exhibit characteristics essential for mimicking transport in biological systems, including subdiffusive dynamics, non-Gaussian displacement distributions, and decoupling of dynamics from material viscoelasticity. Using multiple particle tracking, we identify the physical mechanisms underlying this behavior, which we attribute to a coupling of nanoparticle dynamics to fluctuations in the local network of polymer-linked droplets. Our findings demonstrate the potential of PLEs to serve as fully synthetic mimics of biological transport.

Quantifying the protein-protein association rate in polymer solutions: crowding-induced diffusion and energy modifications

A theoretical framework is developed to study protein-protein association in polymer solutions under diffusion-limited conditions. Starting from the basal association rate, two fundamental aspects concerning macromolecular crowding are particularly taken into account. One is the effect of microviscosity on protein diffusion. The length-scale dependent relations of translational and rotational diffusion coefficients are incorporated. Another is relevant to the crowding-induced effective interaction between the pair of proteins. The resultant energy modifications to the basal association rate are properly introduced, following an instructive classification with increasing crowder size: repulsive interaction dominant, repulsive and attractive interactions competitive, and attractive interaction prevailing. With specific energy modification terms, we are able to investigate the deviations of the association rate from the Stokes-Einstein (SE) behavior (i.e., the linear relationship with respect to the reciprocal of macroviscosity) in a quantitative manner. Our theory is applied to study the association of TEM1-β-lactamase (TEM) and the β-lactamase inhibitor protein (BLIP) in polyethylene glycol (PEG) solutions, with varying concentration and polymerization. We explicitly evaluate the relative association rate constant as a function of the solution macroviscosity. The theoretical results demonstrate very good agreement with the experimental data. Moreover, the complicated non-trivial deviations, either positive (slower than SE) or negative (faster than SE), are systematically rationalized. The precise role of energy modifications and the microviscosity effect on diffusion, in particular on rotational diffusion, are clearly unraveled.

Quantitative assessment of the spatial crowding heterogeneity in cellular fluids

Mammalian cells are crowded with macromolecules, supramolecular complexes, and organelles, all of which equip intracellular fluids, e.g., the cytoplasm, with a dynamic and spatially heterogeneous occupied volume fraction. Diffusion in such fluids has been reported to be heterogeneous, i.e., even individual single-particle trajectories feature spatiotemporally varying transport characteristics. Complementing diffusion-based experiments, we have used here an imaging approach to assess the spatial heterogeneity of the nucleoplasm and the cytoplasm in living interphase cells. As a result, we find that the cytoplasm is more crowded and more heterogeneous than the nucleoplasm on several length scales. This phenomenon even persists in dividing cells, where the mitotic spindle region and its periphery form a contiguous fluid but remain nucleoplasmlike and cytoplasmlike, respectively.

Heterogeneity of crowded cellular fluids on the meso- and nanoscale

Cellular fluids are complex media that are crowded with macromolecules and membrane-enclosed organelles on several length scales. Many studies have shown that crowding can significantly alter transport and reaction kinetics in biological but also in bio-mimetic fluids. Yet, experimental insights on how well bio-mimetic fluids can capture the complexity of cellular fluids are virtually missing. Therefore, we have combined fluorescence correlation spectroscopy (FCS) and fluorescence lifetime imaging microscopy (FLIM) to compare the spatial heterogeneities of biological and simple bio-mimetic crowded fluids. As a result, we find that these artificial fluids are capable of mimicking the average diffusion behavior but not the considerable heterogeneity of cellular fluids on the mesoscale (∼100 nm). On the nanoscale, not even the average properties are captured. Thus, cellular fluids feature a distinct, heterogeneous crowding state that differs from simple bio-mimetic fluids.

Macromolecular Crowding In Vitro, In Vivo, and In Between

Biochemical processes take place in heterogeneous and highly volume-occupied or crowded environments that can considerably influence the reactivity and distribution of participating macromolecules. We summarize here the thermodynamic consequences of excluded-volume and long-range nonspecific intermolecular interactions for macromolecular reactions in volume-occupied media. In addition, we summarize and compare the information content of studies of crowding in vitro and in vivo. We emphasize the importance of characterizing the behavior not only of labeled tracer macromolecules but also the composition and behavior of unlabeled macromolecules in the immediate vicinity of the tracer. Finally, we propose strategies for extending quantitative analyses of crowding in simple model systems to increasingly complex media up to and including intact cells.

Effects of protein crowding on membrane systems

Cellular membranes are typically decorated with a plethora of embedded and adsorbed macromolecules, e.g. proteins, that participate in numerous vital processes. With typical surface densities of 30,000 proteins per μm(2) cellular membranes are indeed crowded places that leave only few nanometers of private space for individual proteins. Here, we review recent advances in our understanding of protein crowding in membrane systems. We first give a brief overview on state-of-the-art approaches in experiment and simulation that are frequently used to study crowded membranes. After that, we review how crowding can affect diffusive transport of proteins and lipids in membrane systems. Next, we discuss lipid and protein sorting in crowded membrane systems, including effects like protein cluster formation, phase segregation, and lipid droplet formation. Subsequently, we highlight recent progress in uncovering crowding-induced conformational changes of membranes, e.g. membrane budding and vesicle formation. Finally, we give a short outlook on potential future developments in the field of crowded membrane systems. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.