May the Road Rise to Meet You: DNA Deformation May Drive DNA Translocation

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Biological systems are rife with polymer translocation events. From the nucleus to the proteosome to the cytoplasmic membrane, long biological polymers of nucleic acids and polypeptides are pulled and pushed across barriers, shuttled to their required destinations by complex machines. This processive movement is often coupled to other functional events, such as the unwinding of helices or the unfolding of polypeptides, and are thus critical to a broad range of cellular activities. Invariably, complexes that track along polymers, particularly along nucleic acids as part of the repair, maintenance, and utilization of the genome, couple the consumption of chemical energy to rectified linear motion along the polymer substrate.

When considering the mechanics of such translocation events, it is easy to think of the polymer as a static track against or along which a motorized complex moves. This is the nature of our mechanical world; roads and rails support the movement of vehicles, and ropes and cables are wound or passed through pulleys and drums. Rarely do the linear tracks play an active role in this relative motion (an exception is the screw).

One of the most dramatic translocation events found in most cells is the packaging of a nucleic acid genome into a protein capsid during the late stages of virus assembly (1). The double-stranded DNA viruses, which include the majority of the estimated 10³¹ bacteriophages in the environment and the eukaryotic herpesviruses, have adapted the ancient additional strand conserved glutamate ring ATPase motif to this task. The packaging ATPases, which in many cases also recruit and process the viral genome for and during packaging, assemble to a vertex of the icosahedral virus capsid, hydrolyze ATP, and package DNA into the capsid to high density, yielding a filled head that serves as the container for the subsequent delivery of the genome to new host cells (Fig. 1). Given the complex chemistry and physics of this process, most models describe the double-stranded DNA (dsDNA) as a relatively inert linear track along which the motor works. But what if the DNA being packaged by viruses and other linear substrates moved by cellular motors are not passive substrates but instead experience conformational distortions that drive their own movement?

Figure 1.

Architecture of a viral DNA packaging motor. In all dsDNA phages and the herpesviruses, a dodecameric portal protein is embedded in a unique fivefold vertex of the head shell. In the well-studied bacteriophage φ29, the pentameric packaging ATPase (blue) is anchored to the capsid through the pentameric prohead RNA (pRNA) scaffold (magenta) and pushes DNA through the dodecameric connector portal (cyan). pRNA is not found in other systems, with the ATPase making direct contact with the portal and/or the head shell. Reprinted from Mao et al. (13) with permission from Elsevier.

This question is addressed by the work of Sharp et al. (2) in this issue. Using molecular dynamics simulations, this article reports that there is the potential that DNA is deformed by its interaction with the portal complex through which DNA is driven into the virus capsid. Viral portals are ubiquitous in the dsDNA phages and their eukaryotic counterparts, such as the herpesviruses, creating the channel through which DNA is pumped into the capsid (3). Unlike the packaging ATPases, portals are imbedded in the capsid shell and remain part of the mature virion, providing the site of attachment for the tail organelle that completes the infectious particle (hence the designation “head-tail connector” in some systems). Portals themselves have a complex functional geometry in that they are dodecameric rings that sit in a pentameric vertex of the capsid and must accommodate the movement of the DNA helix during the packaging and subsequent DNA ejection during infection. Given their close contact with transiting DNA and the packaged DNA as it resides in the head, portals have long been inferred to have an active role in packaging (3, 4).

Whereas other modeling has predicted the deformation of the portal, with projecting luminal loops, crown domains, and charged resides shifting to interact with DNA during its passage (5, 6, 7, 8, 9), Sharp et al. ask how the DNA responds to the portal channel. Earlier work on phage T4 (10) and portals in general (11, 12) suggested that “crunching” or “scrunching” of the DNA helix, the result of the linear force generated by the ATPase ring, or the dehydration effects of the motor complex might be captured and be converted to translocation force. A new look at this by Sharp et al. provides an insightful look at DNA deformation as a means to drive translocation. In two of the portals studied, that of phage T4 and one of the conformers of phage P22, electrostatic interactions between the protein and DNA drive an unpredicted lengthening of the double helix, with the charged DNA backbone being pushed apart by negatively charged regions of the portal. Conversely, the simulation of DNA in the channel of the phage φ29 portal suggests that the helix is compressed linearly, again with deformation driven by the electrostatic potential generated by the protein, in this case by regions of positive charge, yielding an A-form structure seen in other DNA-protein complexes. Neither of these effects depend on DNA sequence, implying that they can act on any substrate.

A comparison of DNA in the channel of two conformers of the P22 portal reveals that alternations between stretched and relaxed DNA, driven by cyclic changes in portal conformation, could support a ratchet mechanism. Given that the ATPase activity of the attendant packaging ATPase is believed to drive cyclic conformational changes in the enzymatic component of the motor, it is conceivable that these changes are propagated through the portal in some manner, providing a cyclic alternation in the electrostatic potential of the portal channel. The spring-like oscillation in the length of the DNA helix caused by the fluctuation in portal structure could be rectified into linear translocation if coupled to a protein-DNA grip and release mechanism whereby the top and bottom of the portal (or the ATPase, which is on the outside of the portal ring) were to essentially store the energy of DNA deformation, releasing it in a controlled, unidirectional manner. This is intriguing. Regardless of what drives conformational change in the portal, the idea that the linear DNA substrate is deformed in a way that makes it an energetic participant in its own movement opens new possibilities for how motors work. Large paddling or rotational motions by motor components may not be required if linear motion can be achieved by stretching or compressing the linear substrate, with rectified, cyclic conformational changes in the DNA rather than lever motions doing the work. If borne out by experiments, further simulation, and more structural information, this proposed mechanism may require a reappraisal of how we think about translocating motors.

Editor: Jason Kahn.