Physical Forces Organizing Biomolecules

V. Adrian Parsegian, PhD, Head, Section on Molecular Biophysics
Jason E. DeRouchey, PhD, Postdoctoral Fellow
Xiangyun Qiu, PhD, Postdoctoral Fellow
Rudolf Podgornik, PhD, Visiting Scientist

With a long-term goal of building a practical physics of biological material, we measure, characterize, and codify the interactions that govern the organization and self-assembly of different types of biological molecules. Connected in part with the recent NIH-wide interest in nanotechnology, we are building on our experience with van der Waals fluctuation forces to formulate interactions involving carbon nanotubes not only in their assembly but also, and more important, as substrates for biopolymers such as DNA. Our undertaking is strengthened by its strong connection with physical theory. Through a series of measurements and analyses of the different types of interactions as revealed in vivo, in vitro, and in computation, we are working with DNA assemblies such as those observed in viral capsids and in vitro; polypeptides and polysaccharides in suspension; and lipid/water liquid crystals. In all these systems, we simultaneously observe the structure of packing and measure intermolecular interaction energies. We have also worked with researchers who create repulsive as well as attractive charge fluctuation forces that have implications for nanotechnology.

van der Waals forces

Parsegian, Podgornik; in collaboration with French, Mkrtchian, Rajter, Ching, Capasso, Munday

Even though van der Waals forces are (1) the dominant interaction that coheres membranes and proteins, (2) the source of the powerful surface tension at membrane interfaces, and (3) the attraction that creates membrane multilayers or allows membranes to adhere to artificial surfaces, the forces are only now undergoing systematic study in a collaboration between quantum physicists and biophysicists. This year, we used the quantum mechanical density functional theory (DFT) solved for several carbon nanotubes in order to compute the forces that cause membranes to cohere and serve as a substrate for many materials. It is remarkable that quantum chemistry combined with our expertise in macromolecular interactions is allowing us to see properties that include torque and force between carbon nanotubes.

By beginning with the elements of physical theory that relate the polarizability of materials to the fluctuations of charges within them, we have been able to design experiments that show how macromolecular organization responds to deliberate changes in solution properties. Progress thus depends on a tight coupling of modern quantum theory of structured materials with experiments and measurements that reveal electromagnetic properties.

We have teamed with groups that measure absorption spectra in order to formulate and compute van der Waals forces involving lipids, water, and ions as well as synthetic structures such as carbon nanotubes. We have shown how charge fluctuation forces conferred by ions in solution can modify forces between lipid membranes. We have measured those forces and computed van der Waals charge fluctuation forces in those same membrane systems. To compute forces between bodies with extended interfaces, we also extended the Lifshitz theory of van der Waals interactions in stratified media such as lipid multilamellar systems. These systems can range from the practical, such as the composite media of electric insulators, to the biological, such as the action of extended polymer layers on biological membranes. In addition, we have developed ways to measure repulsive van der Waals forces in systems in which the properties of the medium are intermediate between those of the interacting bodies. The subsequent ability to create switchable systems offers promising applications in nanotechnology.

Harries D, Rösgen J. A practical guide on how osmolytes modulate macromolecular properties. Methods Cell Biol 2008;84:679-735.
Munday JN, Capasso F, Parsegian VA, Bezrukov SM. Measurements of the Casimir-Lifshitz force in fluids: the effect of electrostatic forces and Debye screening. Phys Rev A 2008;78:032109.
Rajter RF, French RH, Podgornik R, Ching WY, Parsegian VA. Spectral mixing formulations for van der Waals London interactions between multicomponent carbon nanotubes. J Appl Phys 2008;104:053513.
Veble G, Podgornik R. The boundary element approach to van der Waals interactions. Eur Phys J E Soft Matter 2007;23:275-279.
Veble G, Podgornik R. Comparison of density functional theory and field approaches to van der Waals interactions in plan parallel geometry. Phys Rev B 2007;75:155102.

Molecular assembly in vitro and in viruses

Bezrukov, Harries,¹ Parsegian, Petrache,² Podgornik; in collaboration with Stanley, Todd, Rau, Gelbart, Knobler, Zemb

Beginning with direct measurements of forces between large molecules, proceeding with observations of molecules under confinement, and then building on the statistical physics of molecular organization under the action of organizing forces, we have developed new theories and methods of macromolecular organization. One application was to observe DNA under the osmotic stress of large polymers or confined within the hard walls of a virus capsid.

In our most recent work, we observed the ejection of DNA from capsids subjected to various salt conditions. Expansive pressures may vary up to many tens of atmospheres and thus cause initial ejection of DNA. These forces are the product of variable ionic conditions. An unrecognized feature of many viruses is that ionic conditions can penetrate the virus and even modify the expansive force within. At one extreme, DNA in simple salts is under great pressure to expand and be ejected from the capsid; however, under other conditions that permit the DNA-condensing ions to enter the capsid, DNA may be under no expansive pressure. We have begun to measure the motion of DNA within capsids subject to differing ionic conditions and are observing how ejection might be controlled by ionic surroundings. Whether these manipulations ultimately affect viral infectivity is a worthy of pursuit.

To see the connections between DNA pressure and ejection, we have been growing viruses of various lengths for insertion into the same-size capsid. Using X-ray diffraction, we are able to follow the packing and pressure of DNA within the capsid. We have also succeeded in following the condensation of triple-helical DNA, which is implicated in the behavior of telomers. The response to various divalent ions in various tsDNA constructs reveals differences in packing and liquid crystalline tendencies.

Evilevitch A, Fang LT , Yoffe AM , Castelnovo M, Rau DC , Parsegian VA, Gelbart WM, Knobler CM. Effects of salt concentrations and bending energy on the extent of ejection of phage genomes. Biophys J 2008;94:1110-1120.
Parsegian PVA, Podgornik R, French R, Ching W. van der Waals-London dispersion interactions for optically anisotropic cylinders: metallic and semiconducting single-wall carbon nanotubes. Phys Rev B 2007;76:045417.
Petrache HI, Harries D, Parsegian VA. Measurement of lipid forces by X-ray diffraction and osmotic stress. Methods Mol Biol 2007;400:405-419.
Siber A, Dragar M, Parsegian VA, Podgornik R. Packing nanomechanics of viral genomes. Eur Phys J E Soft Matter 2008;26:317-325.
Todd BA, Parsegian VA, Shirahata A, Thomas TJ, Rau DC. Attractive forces between cation condensed DNA double helices. Biophys J 2008;94:4775-4782.

Publications Related to Other Work

Kanduč M, Podgornik R. Electrostatic image effects for counterions between charged planar walls. Eur Phys J E Soft Matter 2007;23:265-274.
Manna F, Lorman V, Podgornik R, Zeks B. Screwlike order, macroscopic chirality, and elastic distortions in high-density DNA mesophases. Phys Rev E 2007;75:030901R.
Stanley C, Krueger S, Parsegian VA, Rau DC. Protein structure and hydration probed by SANS and osmotic stress. Biophys J 2008;94:2777-2789.
Tomić S, Dolanski-Babić S, Vuletić T, Krča S, Ivanović D, Griparić L, Podgornik R. Dielectric relaxation of DNA aqueous solutions. Phys Rev E Stat Nonlin Soft Matter Phys 2007;75:021905.

¹ Daniel Harries, PhD, former Visiting Fellow
² Horia I. Petrache, PhD, former Postdoctoral Fellow

Collaborators

David Andelman, PhD, Tel Aviv University, Tel Aviv, Israel
Sergey M. Bezrukov, PhD, Program in Physical Biology, NICHD, Bethesda, MD
Federico Capasso, PhD, Harvard University, Cambridge, MA
Wai-Yim Ching, PhD, University of Missouri, Kansas City, MO
Joel Cohen, PhD, University of the Pacific, San Francisco, CA
Roger French, PhD, University of Pennsylvania, Philadelphia, PA
William Gelbart, PhD, University of California Los Angeles, Los Angeles, CA
Philip A. Gurnev, PhD, Program in Physical Biology, NICHD, Bethesda, MD
Per Lyngs Hansen, PhD, Syddnask Universitet, Odense, Denmark
Charles Knobler, PhD, University of California Los Angeles, Los Angeles, CA
Jenya Mamasakhlisov, PhD, Yerevan State University, Yerevan, Armenia
Vanik Mkrtchian, PhD, Institute of Physics, National Academy of Sciences, Ashtarak, Armenia
Jeremy Munday, PhD, California Institute of Technology, Pasadena, CA
John F. Nagle, PhD, Carnegie-Mellon University, Pittsburgh, PA
Richard Rajter, BSc, Massachusetts Institute of Technology, Cambridge, MA
Donald C. Rau, PhD, Program in Physical Biology, NICHD, Bethesda, MD
Christopher Stanley, PhD, Center for Neutron Studies, NIST, Gaithersburg, MD
Brian Todd, PhD, Program in Physical Biology, NICHD, Bethesda, MD
Stephanie Tristram-Nagle, PhD, Carnegie-Mellon University, Pittsburgh, PA
Thomas Zemb, PhD, CEA Saclay, Gif-sur-Yvette, France

For further information, contact parsegia@mail.nih.gov or visit http://smb.nichd.nih.gov.