Biophys J, May 2000, p. 2189-2190, Vol. 78, No. 5
NEW AND NOTABLE
Self-Assembly in Vivo
Seth
Fraden* and
Randall D.
Kamien
*Complex Fluids Group, Martin Fisher School of Physics, Brandeis
University, Waltham, Massachusetts 02454, and Department
of Physics and Astronomy, University of Pennsylvania, Philadelphia,
Pennsylvania 19104 USA
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ARTICLE |
The apparent complexity of cellular architecture
can be reduced to the relative simplicity of self-assembled structures.
By virtue of the machinery that produces copious quantities of
identical molecules, some natural structures are the inevitable
consequence of packing constraints enforced by van der Waals,
hydrophobic, and electrostatic forces. The cell lipid bilayer is the
classic example of such a two-dimensional structure. However,
three-dimensional liquid-crystalline arrangements of biomolecules have
been known since the pioneering work of Bouligand (1972)
. Since that
time it has been an outstanding question whether those in vitro motifs that appear in vivo play any significant role in cellular form or
function. Of particular interest is the packing of the genetic material
into a cell. In some cases a millimeter of DNA is packed into a
micron-sized region. While this can lead to a variety of mesophases in
vivo (Livolant, 1991) for cells without nuclei, it is well known that
in the nucleus DNA is wound up onto successive nucleosome core
particles, forming a "beads on a string" complex. It has been an
open question whether nuclear structure is affected by these same
packing considerations.
In a technically challenging work, Livolant and Leforestier (2000)
employed a combination of optical microscopy and freeze-fracture electron microscopy to show that nucleosome core particles (NCPs) form
complex self-assembled structures, even when the DNA linkers have been cut. Freeze-fracture electron microscopy involves slamming delicate liquid crystalline NCP samples at several meters per second
onto a copper block cooled to 10K, followed by etching of the cleaved
surface, and finally producing a replica. Such steps certainly distort
the structure, but over the past 15 years Livolant and co-workers have
developed techniques to control and characterize these artifacts (which
actually are rather small for the NCP but are more significant for pure
DNA phases). Optical and electron microscopy are complementary
techniques; the former provides low resolution but three-dimensional
structure in equilibrated samples, while the latter provides detailed
glimpses of structure on the molecular scale. This work is a masterful
example of how to combine successfully these two microscopies and
raises hope that details of chromosomal structure will be elucidated by
extensions of these same methods.
When macromolecules are in suspension at high densities, such
as those typically found in the cytoplasm or nucleus, packing constraints lead to self-assembly of macromolecules, which then have a
tendency to form orientationally or positionally ordered structures to
maximize entropy. The seemingly paradoxical result of entropy inducing
order has been extensively studied theoretically in the biological
milieu (Herzfeld, 1996). What Livolant and Leforestier have shown is
that in equilibrium at cellular concentrations the NCPs are in complex,
self-assembled structures. Of course, the cell is far from equilibrium,
but to understand cellular structure it is necessary to first
understand the thermodynamic ground state, which is dictated by
minimizing the free energy of the intracellular matrix and which then
acts as a scaffolding on which cellular biochemistry functions and evolves.
The principles of entropically driven parallel ordering of
achiral, rodlike molecules has been understood since Onsager's seminal
work in the 1940s. However, NCPs are cylinders wrapped in several turns
of DNA, which renders the NCPs chiral. When the molecules are chiral,
intermolecular torques create a tendency for the local orientation to
twist in space, frustrating this order. Often this competition is
resolved via the introduction of topological defects. Livolant and
Leforestier (2000) have found that NCPs form germs with a hexagonally
ordered cross section. However, the hexagonal direction appears to
twist along the perpendicular axis. Such twisting of crystalline order
implies the presence of topological defects and suggests a novel
equilibrium structure, the moiré 233 phase (Kamien and Nelson,
1995).
Livolant and Leforestier have found that in vitro the
isolated, cylindrical NCPs stack face-to-face. This is in contrast to the proposed solenoidal packing, which is thought to occur when the
NCPs are strung together in association with 30-nm chromatin fibers
and H1 histone. Thus, like the liquid-crystalline arrangement of
biomolecules in vivo and in vitro, the relevance of this new mesophase
to biological function is unclear. The contrast between this
liquid-crystalline state and the native chromatin structure suggests
that there is further and profound frustration between the geometric
constraints imposed by the continuous DNA strand or H1 and the natural
packing of the NCPs. Comparing the results of this study with ordering
in chromatin with and without H1 is next on the list of the beautiful
experiments we can expect from this group that will move us one step
closer to the goal of understanding chromosomal structure. Indeed, a
physical approach to this problem may help in the resolution of
the question of whether the chromatin is composed of solenoidal
or zigzag fibers.
But further studies of the NCP system may lead to a deeper
understanding of a fundamental, unsolved problem in physics. The relationship between molecular chirality and its macroscopic
manifestation as chiral ordering in liquid crystals remains
poorly understood. There is no theory that can take as input the
structure of a chiral molecule and predict the magnitude, or even the
sign, of the chiral pitch of a liquid crystal. But this system may be
an excellent probe of the connection between intermolecular
orientational correlation and the strength and sign of chiral
interactions (Harris et al., 1999). In this system the DNA can be used
to hinder or enhance these correlations. Because NCPs attached
to a single DNA strand have relative orientations different from those
of NCPs in solution, it should be possible by considering finite chains
to probe the effect of biaxial correlations (considered to be
influential) on the resulting mesoscopic chiral pitch.
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FOOTNOTES |
Received for publication 16 March 2000 and in final form 16 March 2000.
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REFERENCES |
-
Bouligand, Y.
1972.
Twisted fibrous arrangements in biological materials and cholesteric mesophases.
Tissue Cell.
4:189-217[Medline].
-
Harris, A. B.,
R. D. Kamien, and T. C. Lubensky.
1999.
Molecular chirality and chiral parameters.
Rev. Mod. Phys.
71:1745-1757[Abstract/Full Text].
-
Herzfeld, J.
1996.
Entropically driven order in crowded solutions: from liquid crystals to cell biology.
Acc. Chem. Res.
29:31-37.
-
Kamien, R. D., and D. R. Nelson.
1995.
Iterated moir 233 maps and braiding of chiral polymer crystals.
Phys. Rev. Lett.
74:2499-2502.
-
Livolant, F.
1991.
Ordered phases of DNA in vivo and in vitro.
Physica A.
176:117-137.
-
Livolant, F., and A. Leforestier.
2000.
Chiral discotic columnar germs of nucleosome core particles.
Biophys. J.
78:2716-2729[Abstract/Full Text].
Biophys J, May 2000, p. 2189-2190, Vol. 78, No. 5
© 2000 by the Biophysical Society 0006-3495/00/05/2189/02 $2.00
