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First published online July 5, 2006
doi: 10.1242/10.1242/jcs.03063

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How can biochemical reactions within cells differ from those in test tubes?

Section on Physical Biochemistry, Laboratory of Biochemical Pharmacology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA

View larger version (73K): [in a new window]   Fig. 1. Cartoon of eukaryotic cytoplasm magnified 106x. Reproduced from Minton (Minton, 2001a) and modified from Goodsell (Goodsell, 1993).

View larger version (47K): [in a new window]   Fig. 2. Schematic illustration of volume available (blue) and volume excluded (pink and black) to the center of a (A,C) small and (B,D) large spherical molecule added to a solution containing a approximately 30% volume fraction of large spherical molecules (A,B) and the interior of a pore shown in (square) cross-section (C,D). Reproduced from Minton (Minton, 2001a).

View larger version (22K): [in a new window]   Fig. 3. Free energy profiles of a chemical reaction in bulk solution (black curve), in the presence of stabilizing background interactions (green), and in the presence of destabilizing background interactions (red).

View larger version (22K): [in a new window]   Fig. 4. Schematic illustration of how a single set of free energy relationships comprising a thermodynamic cycle may be used to analyze the influence of (A) macromolecular crowding, (B) macromolecular confinement, and (C) macromolecular adsorption upon macromolecular association equilibria.

View larger version (26K): [in a new window]   Fig. 5. (A) Dependence of the solubility of deoxy HbS upon dextran concentration (Bookchin et al., 1999). A 1.75-fold increase in dextran concentration results in a greater than four-fold increase in the equilibrium tendency of deoxy HbS to polymerize. (B) Time course of assembly of HIV capsid protein in the absence () and presence () of 100 g/l Ficoll 70 (del Alamo, 2005). The half-time for assembly of the protein is decreased ten-fold in the presence of Ficoll. (C) Temperature dependence of the ellipticity of -lactalbumin in bulk solution () and encapsulated in hydrated silica sol-gel glass (). The confined protein behaves normally at low temperature, but exhibits only partial unfolding even at temperatures approaching 100°C. Figure reproduced with permission from Eggers and Valentine (Eggers and Valentine, 2001). (D) Time dependence of adsorption of several unrelated proteins to a supported phospholipid bilayer (symbols and solid curves) (Fernandez and Berry, 2003). The dotted curves indicate the time dependence that would be expected in the absence of interaction between adsorbed proteins. The enhanced steepness of the experimentally observed curves (solid) relative to the reference curves (dotted) indicates self-association resulting in clustering of the adsorbed proteins (Minton, 2001b).