Macromolecular Crowding Is More than Hard-Core Repulsions

Cells are crowded, but proteins are almost always studied in dilute aqueous buffer. We review the experimental evidence that crowding affects the equilibrium thermodynamics of protein stability and protein association and discuss the theories employed to explain these observations. In doing so, we highlight differences between synthetic polymers and biologically relevant crowders. Theories based on hard-core interactions predict only crowding-induced entropic stabilization. However, experiment-based efforts conducted under physiologically relevant conditions show that crowding can destabilize proteins and their complexes. Furthermore, quantification of the temperature dependence of crowding effects produced by both large and small cosolutes, including osmolytes, sugars, synthetic polymers, and proteins, reveals enthalpic effects that stabilize or destabilize proteins. Crowding-induced destabilization and the enthalpic component point to the role of chemical interactions between and among the macromolecules, cosolutes, and water. We conclude with suggestions for future studies. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Unusual crowding-induced chain looping kinetics in hard-sphere fluids: a contrastive study with polymer solutions

A theoretical framework is developed to investigate the looping kinetics of a chain in hard-sphere (HS) fluids, based on a generalized Smoluchowski diffusion-reaction equation. A contrastive study with polymer solutions is performed. The crowding-associated effective viscosity and collapse effects are properly taken into account, which obey different scaling relations in HS and polymer fluids. We examine the dependence of the looping time on both concentration and size of crowders, demonstrating unusual and distinct discrepancies in the two crowded media. Firstly, in the solution of large polymers, the looping rate grows monotonically with polymer concentration. On the other hand, in the solution of large HSs, a caging regime can be observed, where the looping time tends to the value in the absence of crowders. Secondly, polymers in moderate size generally impede chain looping due to the enhanced viscosity. However, in HS fluids, the looping time exhibits a rather complicated variation with increasing HS size. We show a possible mechanism where in the case of small crowders with a relatively strong compaction in the probed chain, the looping kinetics can be facilitated. As the crowder size increases, the collapse effect is reduced and looping is dominated by viscosity-induced inhibition. Simultaneously, our theory rationalizes another possibility of the mechanism observed by recent simulation work. We conclude that the looping kinetics in specific systems actually should be governed by the critical competition between the two crowding factors. By giving reasonable measurements of effective viscosity and collapse, our theoretical framework can provide a unified strategy to analyze crowding effects on the looping rate in a systematic manner.

Understanding chain looping kinetics in polymer solutions: crowding effects of microviscosity and collapse

A theoretical framework based on a generalized Langevin equation with fractional Gaussian noise is presented to describe the looping kinetics of chains in polymer solutions. Particular attention is paid to quantitatively revealing crowding effects on the loop formation rate in terms of microviscosity and collapse. By the aid of empirical relations for these two crowding associated physical quantities, we explicitly investigate the relationship between the looping rate and polymer concentration, the degree of polymerization, and system parameters. According to our analysis, the dependence of the looping rate on the crowder volume fraction exhibits three typical regimes: monotonic decreasing, a non-monotonic trend and monotonic increasing. We reveal that these non-trivial behaviors can be attributed to the competition between the two opposing factors of viscosity-associated inhibition and collapse-induced facilitation of loop formation. We apply our theory to analyze the kinetics of single-stranded DNA hairpin base pairing in polyethylene glycol solutions. The theoretical results can reproduce the experimental data on the closing rate of hairpins quantitatively to a certain degree with reasonable fitting parameters. The unexpected increase of the closing rate upon the addition of increasing amounts of polymer is well rationalised. Such good agreements clearly demonstrate the validity of our theory, appropriately addressing the very role of crowding effects in the relevant kinetics.

Single-molecule spectroscopy reveals polymer effects of disordered proteins in crowded environments

Intrinsically disordered proteins (IDPs) are involved in a wide range of regulatory processes in the cell. Owing to their flexibility, their conformations are expected to be particularly sensitive to the crowded cellular environment. Here we use single-molecule Förster resonance energy transfer to quantify the effect of crowding as mimicked by commonly used biocompatible polymers. We observe a compaction of IDPs not only with increasing concentration, but also with increasing size of the crowding agents, at variance with the predictions from scaled-particle theory, the prevalent paradigm in the field. However, the observed behavior can be explained quantitatively if the polymeric nature of both the IDPs and the crowding molecules is taken into account explicitly. Our results suggest that excluded volume interactions between overlapping biopolymers and the resulting criticality of the system can be essential contributions to the physics governing the crowded cellular milieu.