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 have been able to follow up our measurement of the work required to remove water from a complex between the specific DNA binding protein EcoRI and a non-cognate DNA sequence using the osmotic stress approach and a competitive equilibrium binding assay. Our strategy is to couple force measurements between molecules in macroscopic condensed arrays with the interaction of molecules in dilute solution. Our results on complexes of EcoRI with other, nonspecific DNA sequences examined changes in dissociation constant under the osmotic stress. Now we have been able to determine the dissociation rate of the specific complex dissociation rate. The rate slows linearly with osmotic stress and is insensitive to solute identity for a wide range of sizes and chemical natures. The osmotic sensitivity of dissociation is virtually identical to the difference in osmotic sensitivity of specific and nonspecific binding modes of EcoRI. It emerges that: a) Dissociation rates can be used instead of equilibrium assays to measure changes in water sequestered by EcoRI-DNA complexes (to allow us to use much higher osmotic stresses without the complications accompanying equilibrium measurements; b) It is the dehydrated, specifically associated state that is stabilized by osmotic stress or crowding. We have quantified the interaction of small solutes with macromolecular surfaces condensed in ordered macroscopic arrays. From the effect of these small solutes on directly measured forces between DNA double helices and between polysaccharides, we have found that small-molecule solubility varies exponentially with the distance from the macromolecular surface. 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. At the same time we have been doing theoretical physical studies on polyelectrolytes, particularly DNA. We have demonstrated that at the compact densities found in viruses, DNA packs in a liquid-crystal whose angular order is that of a crystal but whose spacings are disorderly like those of a liquid. We have developed an equation of state for DNA assembly in order to relate measured or computed forces to the ways in which the molecules pack. The same interactions between molecules have also been applied to formulate the mechanical stability of long DNA molecules when they bend to come into contact. These forces come into play also in the assembly of DNA with cationic lipids as used in preparations for transfection. Our association with NASA has now developed to the point where we are installing an x-ray lens able to boost photon flux by a factor of 10 to 100 times. We will be using this new lens in our force measurements as well as testing new strategies for x-ray diffraction. - Water, Osmotic stress. Protein/DNA complex, carbohydrate, DNA, molecular forces, x-ray diffraction.
| 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 |
Showing the most recent 10 out of 39 publications
