It is now widely appreciated that almost all proteins and other biological macromolecules in vivo
exist, at least transiently, as components of structural and functional complexes (3
). The number of published studies of macromolecular interactions has increased almost exponentially for the last 20 years and amounts to several hundred a year at present. However, almost all of these studies are aimed at the characterization of attractive interactions that result in the formation of protein complexes or complexes of protein and other macromolecules (e.g. ribonucleoproteins). In contrast, repulsive interactions between macromolecules, by definition, do not lead to the formation of complexes and thus may not be observed directly. However, the presence and significance of repulsive interactions in fluid media containing a high total concentration of macromolecules and/or structural obstacles to the free motion of macromolecules may be observed indirectly through their effects upon a variety of macromolecular reactions involving association and conformational isomerization (49
). Many of these effects may be predicted qualitatively (and sometimes quantitatively) using simple statistical-thermodynamic models, and observed experimentally by measurement of the dependence of thermodynamically-based solution properties and reaction kinetics and equilibria upon the concentration and composition of macromolecular co-solutes that are nominally inert with respect to the reaction of interest. The importance of excluded volume interactions lies in their generality. Such interactions are universal and entirely nonspecific, and have the potential to significantly modulate the kinetics and equilibria of a large number of macromolecular reactions taking place in physiological fluid media.
We shall classify an excluded volume effect according to its origin: macromolecular crowding
refers to effects of volume exclusion by one soluble macromolecule to another, and macromolecular confinement
refers to effects of volume exclusion by a fixed (or confining) boundary to a soluble macromolecule. A number of reviews of both crowding and confinement effects have appeared during the past five years (19
) and it is not our intention to recapitulate published material. Moreover, a separate review of the effect of crowding on macromolecular transport via diffusion appears elsewhere in the present volume. However, in the interest of completeness, in the following section we briefly summarize the various ways that crowding and confinement are expected to influence the equilibria and kinetics of macromolecular associations and isomerizations. Next, results of recently published (2004–2007) theoretical contributions, atomistic simulations, and experiments relating to effects of macromolecular crowding and confinement upon a variety of macromolecular reactions are summarized. (References to work published prior to 2004 may be found in one or more of the reviews cited above.). The present review concludes with discussions of several topics related to the applicability of theoretical predictions or the results of experiments conducted in vitro
to actual macromolecular processes taking place in living organisms.