Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences

Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences

2008 | Huan-Xiang Zhou, Germán Rivas, and Allen P. Minton
Macromolecular crowding and confinement significantly influence biochemical and biophysical processes in living cells. This review summarizes the effects of volume exclusion on macromolecular reactions, equilibria, and the potential physiological consequences of crowding and confinement. It discusses how these effects are studied through theoretical models, simulations, and experiments, and highlights the complexity introduced by heterogeneous environments and nonspecific interactions. Crowding and confinement alter the free energy and equilibrium constants of macromolecular reactions. Crowding, caused by the presence of other macromolecules, reduces the available volume for reactions, increasing the free energy of association and affecting reaction rates. Confinement, due to physical boundaries, restricts the movement of macromolecules, influencing their conformation and reactivity. Both effects are analyzed using thermodynamic models, which relate free energy changes to equilibrium constants. The review covers the effects of crowding on bimolecular association, site-binding, and protein folding. Crowding enhances the association of macromolecules and stabilizes the native state of proteins by reducing the free energy of unfolding. However, the extent of these effects depends on the size and shape of the crowding agents and the macromolecules involved. Similarly, confinement affects the folding rates and stability of proteins, with the extent of stabilization depending on the size and shape of the confining space. Theoretical and experimental studies show that crowding and confinement can significantly influence the kinetics and equilibria of macromolecular reactions. These effects are often studied using models that consider the excluded volume of macromolecules and the interactions between them. The review also discusses the limitations of these models and the need for more detailed simulations and experiments to understand the complex interactions in biological systems. The review emphasizes the importance of considering the effects of crowding and confinement in understanding biological processes, as these factors are prevalent in cellular environments. It highlights the need for further research to bridge the gap between in vitro and in vivo studies, providing a more accurate understanding of the role of these factors in cellular biology.Macromolecular crowding and confinement significantly influence biochemical and biophysical processes in living cells. This review summarizes the effects of volume exclusion on macromolecular reactions, equilibria, and the potential physiological consequences of crowding and confinement. It discusses how these effects are studied through theoretical models, simulations, and experiments, and highlights the complexity introduced by heterogeneous environments and nonspecific interactions. Crowding and confinement alter the free energy and equilibrium constants of macromolecular reactions. Crowding, caused by the presence of other macromolecules, reduces the available volume for reactions, increasing the free energy of association and affecting reaction rates. Confinement, due to physical boundaries, restricts the movement of macromolecules, influencing their conformation and reactivity. Both effects are analyzed using thermodynamic models, which relate free energy changes to equilibrium constants. The review covers the effects of crowding on bimolecular association, site-binding, and protein folding. Crowding enhances the association of macromolecules and stabilizes the native state of proteins by reducing the free energy of unfolding. However, the extent of these effects depends on the size and shape of the crowding agents and the macromolecules involved. Similarly, confinement affects the folding rates and stability of proteins, with the extent of stabilization depending on the size and shape of the confining space. Theoretical and experimental studies show that crowding and confinement can significantly influence the kinetics and equilibria of macromolecular reactions. These effects are often studied using models that consider the excluded volume of macromolecules and the interactions between them. The review also discusses the limitations of these models and the need for more detailed simulations and experiments to understand the complex interactions in biological systems. The review emphasizes the importance of considering the effects of crowding and confinement in understanding biological processes, as these factors are prevalent in cellular environments. It highlights the need for further research to bridge the gap between in vitro and in vivo studies, providing a more accurate understanding of the role of these factors in cellular biology.
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[slides and audio] Macromolecular crowding and confinement%3A biochemical%2C biophysical%2C and potential physiological consequences.