Physical forces between molecules link their structure with the function of biologically important complexes. They let us predict the strength and specificity of interactions among proteins, nucleic acids, lipid bilayers, and carbohydrates. We have found that water structuring plays an unexpectedly large role in the close interaction of all biological systems so far investigated. We think that a new and powerful idea has emerged from these studies. For years we have been seeing hydration interactions between molecules -- DNA double helices, polysaccharides, proteins, lipid bilayers -- that grow exponentially over thelast ten Angstroms approaching contact. These are usually repulisive forces that reflect the work needed to remove solvating waters from the macromolecular surface. What has now become clear is that small molecules -- salts and neutral molecules -- are exponentially distributed in the region near the molecular surface. That is the same water that was difficult to squeeze out between two macromolecules is also water that is more difficult (but sometimes easier) for a small solute to enter. This has been seen with several salts in the Hofmeister series and several neutral polyhydric or zwitterionic solutes that are known to stabilize native protein structures. The magnitude of the interaction of salts correlates with their known effect on water structure, further showing the importance and ubiquity of water structuring forces on the interaction of molecules in solution. The consequence of this is a realization how small molecules can stabilize or destabilize the macromolecule like the Lilliputians in their great number can stabilize (or de-stabilize) a normal creature. We now see a way to unify the study of macromolecular stability by the many smaller ligands and other species that control them. We have measured the dependencies of both the dissociation rate of specifically bound EcoRI endonuclease and the ratio of nonspecific and specific association constants on water activity, salt concentration, and pH in order to distinguish the contributions of these solution components to specific and nonspecific binding. The specific site dissociation rate can be separated into two steps: equilibrium between nonspecific and specific binding of the enzyme to DNA and dissociation of nonspecifically bound protein. About 90% of osmotic dependence of the dissociation rate is due to the specific-nonspecific equilibrium. The residual osmotic sensitivity linked to the dissociation of nonspecifically bound protein depends significantly on the particular osmolyte used indicating a change in solute accessible surface area. In contrast the dissociation of nonspecifically bound enzyme accounts for almost all the pH and salt dependencies. We observed virtually no pH dependence of the specific-nonspecific binding equilibrium measured by the competition assay. The observed weak salt sensitivity of the nonspecific-specific association constant is consistent with an osmotic, rather than electrostatic, action. The seeming lack of a dependence on viscosity suggests the rate-limiting step in dissociation of nonspecifically bound protein is a discrete conformational change rather than a general diffusion of the protein away from the DNA. We are measuring now the osmotic dependence of the EcoRI dissociation rate from two noncognate 'star' sequences and a nonspecific, 'inverted', DNA sequence at very high osmotic stresses. Equilibrium experiments at these high solute concentrations are difficult since the specific site dissociation rate becomes very slow. Kinetic experiments take advantage of these slow rates. The number of waters linked to the dissociation rate of EcoRI from nonspecific DNA sites is consistent with the value inferred from specific sequence dissociation. Even more waters are linked to EcoRI dissociation from 'star' sites at high osmotic stress. More importantly, the average number of waters sequestered by these noncognate complexes decreases with increasing osmotic stress. The extent of dehydration correlates with binding free energy of the complex. The water sequestered by DNA-protein complexes should not be considered fixed and invariant. It can be removed by applying high enough osmotic stress, but the work necessary to dehydrate complexes will naturally depend on the resulting DNA-protein contacts and structure.
| Munday, J N; Capasso, Federico; Parsegian, V Adrian (2009) Measured long-range repulsive Casimir-Lifshitz forces. Nature 457:170-3 |
| Gurnev, Philip A; Harries, Daniel; Parsegian, V Adrian et al. (2009) The dynamic side of the Hofmeister effect: a single-molecule nanopore study of specific complex formation. Chemphyschem 10:1445-9 |
| Cohen, J A; Podgornik, R; Hansen, P L et al. (2009) A phenomenological one-parameter equation of state for osmotic pressures of PEG and other neutral flexible polymers in good solvents. J Phys Chem B 113:3709-14 |
| Petrache, Horia I; Harries, Daniel; Parsegian, V Adrian (2007) Measurement of lipid forces by X-ray diffraction and osmotic stress. Methods Mol Biol 400:405-19 |
| Galanis, Jennifer; Harries, Daniel; Sackett, Dan L et al. (2006) Spontaneous patterning of confined granular rods. Phys Rev Lett 96:028002 |
| Podgornik, R; French, R H; Parsegian, V A (2006) Nonadditivity in van der Waals interactions within multilayers. J Chem Phys 124:044709 |
| Gondre-Lewis, Marjorie C; Petrache, Horia I; Wassif, Christopher A et al. (2006) Abnormal sterols in cholesterol-deficiency diseases cause secretory granule malformation and decreased membrane curvature. J Cell Sci 119:1876-85 |
| Harries, Daniel; Podgornik, Rudi; Parsegian, V Adrian et al. (2006) Ion induced lamellar-lamellar phase transition in charged surfactant systems. J Chem Phys 124:224702 |
| Petrache, Horia I; Zemb, Thomas; Belloni, Luc et al. (2006) Salt screening and specific ion adsorption determine neutral-lipid membrane interactions. Proc Natl Acad Sci U S A 103:7982-7 |
| Petrache, Horia I; Tristram-Nagle, Stephanie; Harries, Daniel et al. (2006) Swelling of phospholipids by monovalent salt. J Lipid Res 47:302-9 |
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