Macromolecular Crowding and Confinement: Biochemical, Biophysical, and Potential Physiological Consequences

Abstract

Expected and observed effects of volume exclusion on the free energy of rigid and flexible macromolecules in crowded and confined systems, and consequent effects of crowding and confinement on macromolecular reaction rates and equilibria are summarized. Findings from relevant theoretical/simulation and experimental literature published from 2004 onward are reviewed. Additional complexity arising from the heterogeneity of local environments in biological media, and the presence of nonspecific interactions between macromolecules over and above steric repulsion are discussed. Theoretical and experimental approaches to the characterization of crowding-and confinement-induced effects in systems approaching the complexity of living organisms are suggested.

Shear-Driven Redistribution of Surfactant Affects Enzyme Activity in Well-Mixed Femtoliter Droplets

“…Although PEG600 is not surface active, at the high concentrations used, we expect the interface would be occupied primarily by PEG600 molecules due to excluded volume effects and reduced diffusion coefficients. 7 In addition, PEG600 can form extended hydrogen-bonded networks with the NP-PEG surfactant molecules already present at the interface. 8 It is well known that molecular crowding affects reaction rates, however, these effects should depend primarily on the concentration of crowders in the aqueous environment, not on the size of the reaction vessel (droplet) itself, and should therefore be the same (within experimental uncertainty) for large and small droplets, as well as the bulk, as long as the concentration of crowders were the same.…”

RNA Hairpin Folding in the Crowded Cell

“…In this way, the so‐called excluded volume effect stabilizes the more compact folded native state relative to the unfolded more extended state. The magnitude of this effect depends on the relative size of the RNA and the crowder 4b, 6a, 7. Thus, the most stabilizing effects of macromolecular crowding agents were found for tertiary and quaternary RNA structures.…”

Mineralization and non-ideality: on nature’s foundry

“…Macromolecular confinement refers to the behavior of a solute with respect to volume exclusion by a fixed boundary (e.g., cytoplasmic meshwork or extracellular matrix), whereas macromolecular crowding refers to effects of volume exclusion with reference to inter-solute interactions (Zhou et al 2008). Confinement of macromolecules within recesses or pores can result in significant size-and shape-dependent changes of solute chemical potential.…”

“…In view of the physicochemistry of cellular life, 'microspaces' with multicomponent, multiphase and crowded conditions in aqueous electrolytes are presumed crucial for enabling sustained biochemical processes (Spitzer et al 2015;Spitzer and Poolman 2009). Such crowded and confined environments render macromolecular reaction rates and equilibria complex, especially in view of the heterogeneous composition of biological spaces (Zhou et al 2008). At the mesoscale, the impact of non-ideality is evident from the liquid-like behavior of membraneless cellular components (Brangwynne et al 2009Hyman and Brangwynne 2011).…”

“…Associated subcellular phase transitions fundamentally alter the perception of biomolecular interactions and bring to the center-stage the multiphasic aspects of biochemical regulation. Although chemical non-ideality is vital for cellular processes (Minton 2001;Zhou et al 2008), several in vitro experiments often apply relatively low contents of biomolecular reactants and may neglect a faithful replication of the biophysical scenario. Therefore, the states and dynamics of the physico-chemistry in niche biological environments can offer significant insights into the workings of life.…”