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MOLECULAR BIOLOGY: ON MACROMOLECULAR CROWDING

The following points are made by Allen P. Minton (Current Biology 2006 16:R269):

1) The term "macromolecular crowding" was coined to connote the influence of mutual volume exclusion upon the energetics and transport properties of macromolecules within a crowded, or highly volume-occupied, medium. Because of steric repulsion, no part of any two macromolecules can be in the same place at the same time. That part of the total volume which cannot be occupied by the center of mass of a particular solute species at a particular instant is called the "excluded volume", and the part of total volume that may be occupied is called the "available volume". As the fraction of volume occupied by macromolecules of a given size increases, the fraction of volume available to an additional macromolecule of comparable size decreases rapidly, and becomes much less than the fraction of volume available to solvent (water).

2) In freshman chemistry we are taught that the reactivity of a solute is proportional to its concentration, or number of molecules of solute per unit total volume. In fact, this is only strictly true in the highly dilute limit. In a highly volume-occupied solution, the reactivity of a test solute species is determined by the number of molecules of that solute per unit of available volume, which is an effective concentration called the "thermodynamic activity". Depending upon the size and shape of the test solute species, and the number density and sizes and shapes of all of the macromolecular solute species in the vicinity of the test species -- termed "background species" --the effective concentration or activity of the test species may exceed its actual concentration by as much as several orders of magnitude.

3) Biochemical rates and equilibria have traditionally been studied in dilute solution, where the consequences of steric repulsion between solutes are generally negligibly small. In contrast, almost all fluid media in biology contain a high total volume fraction of macromolecules. In special cases, a medium consists primarily of a single species of macromolecule -- for example, hemoglobin in hemolysate or albumin in blood serum --but more commonly the medium is highly heterogeneous, as in the case of prokaryotic cytoplasm, containing a mixture of proteins, nucleic acids and polysaccharides in varying proportion. Experiments carried out on solutions containing comparable volume fractions of purified proteins or chemically inert polysaccharides have demonstrated that excluded volume effects in such media can result in the alteration of equilibrium and rate constants by up to several orders of magnitude.

4) Crowding is a consequence of steric repulsion, a destabilizing interaction that increases the total free energy or work content of the system. Equilibrium theory predicts that if the composition of a system can change to minimize the total free energy of that system, it will do so. Thus crowding is expected to shift equilibria toward a state of the system in which excluded volume is minimized. The extent to which a particular macromolecular species excludes volume to its neighbors generally increases with the ratio of surface to volume of that species. Hence crowding exerts a generalized pressure for the reduction of the surface to volume ratio. This is accomplished in two ways. The first is by favoring compact conformations over extended conformations of flexible macromolecules. The second is by favoring both specific macromolecular associations leading to the formation of well-defined oligomeric species, and nonspecific macromolecular associations leading to the formation of large aggregates of native or nonnative species.[1-4]

References:

1. R.J. Ellis, Macromolecular crowding: obvious but underappreciated, Trends Biochem. Sci. 26 (2001), pp. 597 604

2. A.P. Minton, The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media, J. Biol. Chem. 276 (2001), pp. 10577 10580

3. A.P. Minton, Influence of macromolecular crowding upon the stability and state of association of proteins: predictions and associations, J. Pharm. Sci. 94 (2005), pp. 1668 1675

4. G.B. Ralston, Effects of crowding in protein solutions, J. Chem. Educ. 67 (1990), pp. 857 860

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