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.

Figure 1

Thermodynamic cycles illustrating linkage between free energy of transfer of reactants and products from dilute solution to crowded medium and standard free energy of (A) association in solution, (B) site-binding, and (C) two-state folding of a protein.

Figure 1

Thermodynamic cycles illustrating linkage between free energy of transfer of reactants and products from dilute solution to crowded medium and standard free energy of (A) association in solution, (B) site-binding, and (C) two-state folding of a protein.

Figure 1

Thermodynamic cycles illustrating linkage between free energy of transfer of reactants and products from dilute solution to crowded medium and standard free energy of (A) association in solution, (B) site-binding, and (C) two-state folding of a protein.

Figure 2

Thermodynamic cycles illustrating linkage between free energy of transfer of reactants and products from dilute solution to confined volume element and standard free energy of (A) association in solution, (B) site-binding, and (C) two-state folding of a protein.

Figure 2

Thermodynamic cycles illustrating linkage between free energy of transfer of reactants and products from dilute solution to confined volume element and standard free energy of (A) association in solution, (B) site-binding, and (C) two-state folding of a protein.

Figure 2

Thermodynamic cycles illustrating linkage between free energy of transfer of reactants and products from dilute solution to confined volume element and standard free energy of (A) association in solution, (B) site-binding, and (C) two-state folding of a protein.

Figure 3

Effect of volume fraction φ of hard sphere crowders upon equilibrium constant for association of two spherical monomers with R₁ = 1 to form a spherocylindrical dimer with twice the volume, and (a) L₂ = 0, R₂ = 1.26 (spherical dimer); (b) L₂ = 2/3, R₂ = 1; (c) L₂ = 1, R₂ = 0.928; (d) L₂ = 1.5, R₂ = 0.851; and (e) L₂ = 2, R₂ = 0.794.

Figure 4

Effect of volume fraction φ of hard sphere crowders upon equilibrium constant for binding of a spherical macromolecular ligand to an immobile surface site. MW_ligand/MW_crowder = 2 (curve a), 1 (curve b), and 0.5 (curve c).

Figure 5

Effect of confinement in a spherical cavity upon the free energy of two-state folding, calculated as a function of cavity radius according to the theory of Zhou and Dill (90), for proteins containing N = 100 residues (a) and 200 residues (b). Vertical lines represent the radii of the hard spherical representation of the folded proteins, calculated according to r_N (Å) = 3.73 N^1/3. The radius of gyration of the unfolded protein is calculated according to r_g (Å) = 3.27 N^1/2.