The bacteriophage genome undergoes a succession of intracapsid phase transitions upon DNA ejection

The structure and physical properties of a packaged bacteriophage particle

A string of nucleotides confined within a protein capsid contains all the instructions necessary to make a functional virus particle, a virion. Although the structure of the protein capsid is known for many virus species1,2, the three-dimensional organization of viral genomes has mostly eluded experimental probes3,4. Here we report all-atom structural models of an HK97 virion5, including its entire 39,732 base pair genome, obtained through multiresolution simulations. Mimicking the action of a packaging motor6, the genome was gradually loaded into the capsid. The structure of the packaged capsid was then refined through simulations of increasing resolution, which produced a 26 million atom model of the complete virion, including water and ions confined within the capsid. DNA packaging occurs through a loop extrusion mechanism7 that produces globally different configurations of the packaged genome and gives each viral particle individual traits. Multiple microsecond-long all-atom simulations characterized the effect of the packaged genome on capsid structure, internal pressure, electrostatics and diffusion of water, ions and DNA, and revealed the structural imprints of the capsid onto the genome. Our approach can be generalized to obtain complete all-atom structural models of other virus species, thereby potentially revealing new drug targets at the genome-capsid interface.

Temperature-induced DNA density transition in phage λ capsid revealed with contrast-matching SANS

Structural details of a genome packaged in a viral capsid are essential for understanding how the structural arrangement of a viral genome in a capsid controls its release dynamics during infection, which critically affects viral replication. We previously found a temperature-induced, solid-like to fluid-like mechanical transition of packaged λ-genome that leads to rapid DNA ejection. However, an understanding of the structural origin of this transition was lacking. Here, we use small-angle neutron scattering (SANS) to reveal the scattering form factor of dsDNA packaged in phage λ capsid by contrast matching the scattering signal from the viral capsid with deuterated buffer. We used small-angle X-ray scattering and cryoelectron microscopy reconstructions to determine the initial structural input parameters for intracapsid DNA, which allows accurate modeling of our SANS data. As result, we show a temperature-dependent density transition of intracapsid DNA occurring between two coexisting phases-a hexagonally ordered high-density DNA phase in the capsid periphery and a low-density, less-ordered DNA phase in the core. As the temperature is increased from 20 °C to 40 °C, we found that the core-DNA phase undergoes a density and volume transition close to the physiological temperature of infection (~37 °C). The transition yields a lower energy state of DNA in the capsid core due to lower density and reduced packing defects. This increases DNA mobility, which is required to initiate rapid genome ejection from the virus capsid into a host cell, causing infection. These data reconcile our earlier findings of mechanical DNA transition in phage.

Lipidic lyotropic liquid crystals: Insights on biomedical applications

Liquid crystals (LCs) possess unique physicochemical properties, translatable into a wide range of applications. To date, lipidic lyotropic LCs (LLCs) have been extensively explored in drug delivery and imaging owing to the capability to encapsulate and release payloads with different characteristics. The current landscape of lipidic LLCs in biomedical applications is provided in this review. Initially, the main properties, types, methods of fabrication and applications of LCs are showcased. Then, a comprehensive discussion of the main biomedical applications of lipidic LLCs accordingly to the application (drug and biomacromolecule delivery, tissue engineering and molecular imaging) and route of administration is examined. Further discussion of the main limitations and perspectives of lipidic LLCs in biomedical applications are also provided. STATEMENT OF SIGNIFICANCE: Liquid crystals (LCs) are those systems between a solid and liquid state that possess unique morphological and physicochemical properties, translatable into a wide range of biomedical applications. A short description of the properties of LCs, their types and manufacturing procedures is given to serve as a background to the topic. Then, the latest and most innovative research in the field of biomedicine is examined, specifically the areas of drug and biomacromolecule delivery, tissue engineering and molecular imaging. Finally, prospects of LCs in biomedicine are discussed to show future trends and perspectives that might be utilized. This article is an ampliation, improvement and actualization of our previous short forum article "Bringing lipidic lyotropic liquid crystal technology into biomedicine" published in TIPS.

Structural changes in bacteriophage T7 upon receptor-induced genome ejection

Many tailed bacteriophages assemble ejection proteins and a portal-tail complex at a unique vertex of the capsid. The ejection proteins form a transenvelope channel extending the portal-tail channel for the delivery of genomic DNA in cell infection. Here, we report the structure of the mature bacteriophage T7, including the ejection proteins, as well as the structures of the full and empty T7 particles in complex with their cell receptor lipopolysaccharide. Our near-atomic-resolution reconstruction shows that the ejection proteins in the mature T7 assemble into a core, which comprises a fourfold gene product 16 (gp16) ring, an eightfold gp15 ring, and a putative eightfold gp14 ring. The gp15 and gp16 are mainly composed of helix bundles, and gp16 harbors a lytic transglycosylase domain for degrading the bacterial peptidoglycan layer. When interacting with the lipopolysaccharide, the T7 tail nozzle opens. Six copies of gp14 anchor to the tail nozzle, extending the nozzle across the lipopolysaccharide lipid bilayer. The structures of gp15 and gp16 in the mature T7 suggest that they should undergo remarkable conformational changes to form the transenvelope channel. Hydrophobic α-helices were observed in gp16 but not in gp15, suggesting that gp15 forms the channel in the hydrophilic periplasm and gp16 forms the channel in the cytoplasmic membrane.

Effects of Model Shape, Volume, and Softness of the Capsid for DNA Packaging of phi29

Double-stranded DNA is under extreme confinement when packed in phage phi29 with osmotic pressures approaching 60 atm and densities near liquid crystalline. The shape of the capsid determined from experiment is elongated. We consider the effects of the capsid shape and volume on the DNA distribution. We propose simple models for the capsid of phage phi29 to capture volume, shape, and wall flexibility, leading to an accurate DNA density profile. The effect of the packaging motor twisting the DNA on the resulting density distribution has been explored. We find packing motor induced twisting leads to a greater numbers of defects formed. The emergence of defects such as bubbles or large roll angles along the DNA shows a sequence dependence, and the resulting flexibility leads to an inhomogeneous distribution of defects occurring more often at TpA steps and AT-rich regions. In conjunction with capsid elongation, this has effects on the global DNA packing structures.

Liquid Crystal Peptide/DNA Coacervates in the Context of Prebiotic Molecular Evolution

Liquid–liquid phase separation (LLPS) phenomena are ubiquitous in biological systems, as various cellular LLPS structures control important biological processes. Due to their ease of in vitro assembly into membraneless compartments and their presence within modern cells, LLPS systems have been postulated to be one potential form that the first cells on Earth took on. Recently, liquid crystal (LC)-coacervate droplets assembled from aqueous solutions of short double-stranded DNA (s-dsDNA) and poly-L-lysine (PLL) have been reported. Such LC-coacervates conjugate the advantages of an associative LLPS with the relevant long-range ordering and fluidity properties typical of LC, which reflect and propagate the physico-chemical properties of their molecular constituents. Here, we investigate the structure, assembly, and function of DNA LC-coacervates in the context of prebiotic molecular evolution and the emergence of functional protocells on early Earth. We observe through polarization microscopy that LC-coacervate systems can be dynamically assembled and disassembled based on prebiotically available environmental factors including temperature, salinity, and dehydration/rehydration cycles. Based on these observations, we discuss how LC-coacervates can in principle provide selective pressures effecting and sustaining chemical evolution within partially ordered compartments. Finally, we speculate about the potential for LC-coacervates to perform various biologically relevant properties, such as segregation and concentration of biomolecules, catalysis, and scaffolding, potentially providing additional structural complexity, such as linearization of nucleic acids and peptides within the LC ordered matrix, that could have promoted more efficient polymerization. While there are still a number of remaining open questions regarding coacervates, as protocell models, including how modern biologies acquired such membraneless organelles, further elucidation of the structure and function of different LLPS systems in the context of origins of life and prebiotic chemistry could provide new insights for understanding new pathways of molecular evolution possibly leading to the emergence of the first cells on Earth.

Novel Trends in Lyotropic Liquid Crystals

We introduce and shortly summarize a variety of more recent aspects of lyotropic liquid crystals (LLCs), which have drawn the attention of the liquid crystal and soft matter community and have recently led to an increasing number of groups studying this fascinating class of materials, alongside their normal activities in thermotopic LCs. The diversity of topics ranges from amphiphilic to inorganic liquid crystals, clays and biological liquid crystals, such as viruses, cellulose or DNA, to strongly anisotropic materials such as nanotubes, nanowires or graphene oxide dispersed in isotropic solvents. We conclude our admittedly somewhat subjective overview with materials exhibiting some fascinating properties, such as chromonics, ferroelectric lyotropics and active liquid crystals and living lyotropics, before we point out some possible and emerging applications of a class of materials that has long been standing in the shadow of the well-known applications of thermotropic liquid crystals, namely displays and electro-optic devices.

Quantitative Study of the Chiral Organization of the Phage Genome Induced by the Packaging Motor

Molecular motors that translocate DNA are ubiquitous in nature. During morphogenesis of double-stranded DNA bacteriophages, a molecular motor drives the viral genome inside a protein capsid. Several models have been proposed for the three-dimensional geometry of the packaged genome, but very little is known of the signature of the molecular packaging motor. For instance, biophysical experiments show that in some systems, DNA rotates during the packaging reaction, but most current biophysical models fail to incorporate this property. Furthermore, studies including rotation mechanisms have reached contradictory conclusions. In this study, we compare the geometrical signatures imposed by different possible mechanisms for the packaging motors: rotation, revolution, and rotation with revolution. We used a previously proposed kinetic Monte Carlo model of the motor, combined with Brownian dynamics simulations of DNA to simulate deterministic and stochastic motor models. We find that rotation is necessary for the accumulation of DNA writhe and for the chiral organization of the genome. We observe that although in the initial steps of the packaging reaction, the torsional strain of the genome is released by rotation of the molecule, in the later stages, it is released by the accumulation of writhe. We suggest that the molecular motor plays a key role in determining the final structure of the encapsidated genome in bacteriophages.

Fine structure of viral dsDNA encapsidation

Unraveling the mechanisms of packing of DNA inside viral capsids is of fundamental importance to understanding the spread of viruses. It could also help develop new applications to targeted drug delivery devices for a large range of therapies. In this article, we present a robust, predictive mathematical model and its numerical implementation to aid the study and design of bacteriophage viruses for application purposes. Exploiting the analogies between the columnar hexagonal chromonic phases of encapsidated viral DNA and chromonic aggregates formed by plank-shaped molecular compounds, we develop a first-principles effective mechanical model of DNA packing in a viral capsid. The proposed expression of the packing energy, which combines relevant aspects of the liquid crystal theory, is developed from the model of hexagonal columnar phases, together with that describing configurations of polymeric liquid crystals. The method also outlines a parameter selection strategy that uses available data for a collection of viruses, aimed at applications to viral design. The outcome of the work is a mathematical model and its numerical algorithm, based on the method of finite elements, and computer simulations to identify and label the ordered and disordered regions of the capsid and calculate the inner pressure. It also presents the tools for the local reconstruction of the DNA "scaffolding" and the center curve of the filament within the capsid.

Chromosomal Organization and Regulation of Genetic Function in Escherichia coli Integrates the DNA Analog and Digital Information

In this article, we summarize our current understanding of the bacterial genetic regulation brought about by decades of studies using the Escherichia coli model. It became increasingly evident that the cellular genetic regulation system is organizationally closed, and a major challenge is to describe its circular operation in quantitative terms. We argue that integration of the DNA analog information (i.e., the probability distribution of the thermodynamic stability of base steps) and digital information (i.e., the probability distribution of unique triplets) in the genome provides a key to understanding the organizational logic of genetic control. During bacterial growth and adaptation, this integration is mediated by changes of DNA supercoiling contingent on environmentally induced shifts in intracellular ionic strength and energy charge. More specifically, coupling of dynamic alterations of the local intrinsic helical repeat in the structurally heterogeneous DNA polymer with structural-compositional changes of RNA polymerase holoenzyme emerges as a fundamental organizational principle of the genetic regulation system. We present a model of genetic regulation integrating the genomic pattern of DNA thermodynamic stability with the gene order and function along the chromosomal OriC-Ter axis, which acts as a principal coordinate system organizing the regulatory interactions in the genome.

Structure and the role of filling rate on model dsDNA packed in a phage capsid

The conformation of DNA inside bacteriophages is of paramount importance for understanding packaging and ejection mechanisms. Models describing the structure of the confined macromolecule have depicted highly ordered conformations, such as spooled or toroidal arrangements that focus on reproducing experimental results obtained by averaging over thousands of configurations. However, it has been seen that more disordered states, including DNA kinking and the presence of domains with different DNA orientation can also accurately reproduce many of the structural experiments. In this work we have compared the results obtained through different simulated filling rates. We find a rate dependence for the resulting constrained states showing different anisotropic configurations. We present a quantitative analysis of the density distribution and the DNA orientation across the capsid showing excellent agreement with structural experiments. Second, we have analyzed the correlations within the capsid, finding evidence of the presence of domains characterized by aligned segments of DNA characterized by the structure factor. Finally, we have measured the number and distribution of DNA defects such as the emergence of bubbles and kinks as function of the filling rate. We find the slower the rate the fewer kink defects that appear and they would be unlikely at experimental filling rates with our model parameters. DNA domains of various orientation get larger with slower rates.

Modelling and DNA topology of compact 2-start and 1-start chromatin fibres

We have investigated the structure of the most compact 30-nm chromatin fibres by modelling those with 2-start or 1-start crossed-linker organisations. Using an iterative procedure we obtained possible structural solutions for fibres of the highest possible compaction permitted by physical constraints, including the helical repeat of linker DNA. We find that this procedure predicts a quantized nucleosome repeat length (NRL) and that only fibres with longer NRLs (≥197 bp) can more likely adopt the 1-start organisation. The transition from 2-start to 1-start fibres is consistent with reported differing binding modes of the linker histone. We also calculate that in 1-start fibres the DNA constrains more torsion (as writhe) than 2-start fibres with the same NRL and that the maximum constraint obtained is in accord with previous experimental results. We posit that the coiling of the fibre is driven by overtwisting of linker DNA which, in the most compact forms - for example, in echinoderm sperm and avian erythrocytes - could adopt a helical repeat of ∼10 bp/turn. We argue that in vivo the total twist of linker DNA could be modulated by interaction with other abundant chromatin-associated proteins and by epigenetic modifications of the C-terminal tail of linker histones.

Capsid expansion of bacteriophage T5 revealed by high resolution cryoelectron microscopy

The large (90-nm) icosahedral capsid of bacteriophage T5 is composed of 775 copies of the major capsid protein (mcp) together with portal, protease, and decoration proteins. Its assembly is a regulated process that involves several intermediates, including a thick-walled round precursor prohead that expands as the viral DNA is packaged to yield a thin-walled and angular mature capsid. We investigated capsid maturation by comparing cryoelectron microscopy (cryo-EM) structures of the prohead, the empty expanded capsid both with and without decoration protein, and the virion capsid at a resolution of 3.8 Å for the latter. We detail the molecular structure of the mcp, its complex pattern of interactions, and their evolution during maturation. The bacteriophage T5 mcp is a variant of the canonical HK97-fold with a high level of plasticity that allows for the precise assembly of a giant macromolecule and the adaptability needed to interact with other proteins and the packaged DNA.

Spontaneous Domain Formation in Spherically Confined Elastic Filaments

Although the free energy of a genome packing into a virus is dominated by DNA-DNA interactions, ordering of the DNA inside the capsid is elasticity driven, suggesting general solutions with DNA organized into spool-like domains. Using analytical calculations and computer simulations of a long elastic filament confined to a spherical container, we show that the ground state is not a single spool as assumed hitherto, but an ordering mosaic of multiple homogeneously ordered domains. At low densities, we observe concentric spools, while at higher densities, other morphologies emerge, which resemble topological links. We discuss our results in the context of metallic wires, viral DNA, and flexible polymers.

Type-I collagen fibrils: From growth morphology to local order

The length of type-I collagen fibrils in solution increases through the development and progress of pointed tips appearing successively at the two ends of an axis-symmetric shaft with constant diameter. Those tips, respectively fine ([Formula: see text]) or coarse ([Formula: see text]) have opposite molecular orientations. The [Formula: see text]-pointed tips, the first to appear, are particularly remarkable as they all show, on most of their length, a common parabolic profile which stays constant during the growth. Assuming that the latter occurs by lateral accretion of individual molecules in staggered configuration, we propose to give account of this prominent morphological feature along a purely geometrical argument, the profile of a tip being linked to the shape of the trajectories followed all along the accretion process. Among several possible trajectories, Fermat spirals lead to a parabolic profile in perfect agreement with the one observed for [Formula: see text]-pointed tips. This is to be put in relation with the presence of such spirals in phyllotactic patterns which ensure the best packing efficiency in cases of axis-symmetry, which is indeed that of dense collagen fibrils. Moreover, those patterns are structured by concentric circles of dislocations, constitutive of the structure itself, whose behaviour might contribute to the mechanical properties of the fibrils.

Cryo-EM structure and in vitro DNA packaging of a thermophilic virus with supersized T=7 capsids

Understanding molecular events during virus assembly and genome packaging is important for understanding viral life cycles, and the functioning of other protein–nucleic acid machines. The model system developed for the thermophilic bacteriophage P23-45 offers advantages over other systems. Cryo-EM reconstructions reveal modifications to a canonical capsid protein fold, resulting in capsids that are abnormally large for this virus class. Structural information on the portal protein, through which the genome is packaged, demonstrates that the capsid influences the portal’s conformation. This has implications for understanding how processes inside and outside the capsid can be coordinated.

Double-stranded DNA viruses, including bacteriophages and herpesviruses, package their genomes into preformed capsids, using ATP-driven motors. Seeking to advance structural and mechanistic understanding, we established in vitro packaging for a thermostable bacteriophage, P23-45 of Thermus thermophilus. Both the unexpanded procapsid and the expanded mature capsid can package DNA in the presence of packaging ATPase over the 20 °C to 70 °C temperature range, with optimum activity at 50 °C to 65 °C. Cryo-EM reconstructions for the mature and immature capsids at 3.7-Å and 4.4-Å resolution, respectively, reveal conformational changes during capsid expansion. Capsomer interactions in the expanded capsid are reinforced by formation of intersubunit β-sheets with N-terminal segments of auxiliary protein trimers. Unexpectedly, the capsid has T=7 quasi-symmetry, despite the P23-45 genome being twice as large as those of known T=7 phages, in which the DNA is compacted to near-crystalline density. Our data explain this anomaly, showing how the canonical HK97 fold has adapted to double the volume of the capsid, while maintaining its structural integrity. Reconstructions of the procapsid and the expanded capsid defined the structure of the single vertex containing the portal protein. Together with a 1.95-Å resolution crystal structure of the portal protein and DNA packaging assays, these reconstructions indicate that capsid expansion affects the conformation of the portal protein, while still allowing DNA to be packaged. These observations suggest a mechanism by which structural events inside the capsid can be communicated to the outside.

Influence of Microscopic Interactions on the Flexible Mechanical Properties of Viral DNA

During the packaging and ejection of viral DNA, its mechanical properties play an essential role in viral infection. Some of these mechanical properties originate from different microscopic interactions of the encapsulated DNA in the capsid. Based on an updated mesoscopic model of the interaction potential by Parsegian et al., an alternative continuum elastic model of the free energy of the confined DNA in the capsid is developed in this work. With this model, we not only quantitatively identify the respective contributions from hydration repulsion, electrostatic repulsion, entropy and elastic bending but also predict the ionic effect of viral DNA's mechanical properties during the packaging and ejection. The relevant predictions are quantitively or qualitatively consistent with the existing experimental results. Furthermore, the nonmonotonous or monotonous changes in the respective contributions of microscopic interactions to the ejection force and free energy at different ejection stages are revealed systematically. Among these, the nonmonotonicity in the entropic contribution implies a transition of viral DNA structure from order to disorder during the ejection.

Direct Liquid to Crystal Transition in a Quasi-Two-Dimensional Colloidal Membrane

Using synchrotron-based small-angle X-ray scattering, we study rigid fd viruses assembled into isolated monolayers from mixtures with a nonabsorbing polymer, which acts as an osmotic agent. As the polymer concentration increases, we observe a direct liquid to crystal transition, without an intermediate hexatic phase, in contrast with many other similar systems, such as concentrated DNA phases or packings of surfactant micelles. We tentatively attribute this effect to the difference in stiffness. The liquid phase can be well described by a hard-disk fluid, while we model the crystalline one as a hexagonal harmonic lattice and we evaluate its elastic constants.

Human herpesvirus portal proteins: Structure, function, and antiviral prospects

Herpesviruses (Herpesvirales) and tailed bacteriophages (Caudovirales) package their dsDNA genomes through an evolutionarily conserved mechanism. Much is known about the biochemistry and structural biology of phage portal proteins and the DNA encapsidation (viral genome cleavage and packaging) process. Although not at the same level of detail, studies on HSV-1, CMV, VZV, and HHV-8 have revealed important information on the function and structure of herpesvirus portal proteins. During dsDNA phage and herpesviral genome replication, concatamers of viral dsDNA are cleaved into single length units by a virus-encoded terminase and packaged into preformed procapsids through a channel located at a single capsid vertex (portal). Oligomeric portals are formed by the interaction of identical portal protein monomers. Comparing portal protein primary aa sequences between phage and herpesviruses reveals little to no sequence similarity. In contrast, the secondary and tertiary structures of known portals are remarkable. In all cases, function is highly conserved in that portals are essential for DNA packaging and also play a role in releasing viral genomic DNA during infection. Preclinical studies have described small molecules that target the HSV-1 and VZV portals and prevent viral replication by inhibiting encapsidation. This review summarizes what is known concerning the structure and function of herpesvirus portal proteins primarily based on their conserved bacteriophage counterparts and the potential to develop novel portal-specific DNA encapsidation inhibitors.

Photochemical analysis of structural transitions in DNA liquid crystals reveals differences in spatial structure of DNA molecules organized in liquid crystalline form

The anisotropic shape of DNA molecules allows them to form lyotropic liquid crystals (LCs) at high concentrations. This liquid crystalline arrangement is also found in vivo (e.g., in bacteriophage capsids, bacteria or human sperm nuclei). However, the role of DNA liquid crystalline organization in living organisms still remains an open question. Here we show that in vitro, the DNA spatial structure is significantly changed in mesophases compared to non-organized DNA molecules. DNA LCs were prepared from pBluescript SK (pBSK) plasmid DNA and investigated by photochemical analysis of structural transitions (PhAST). We reveal significant differences in the probability of UV-induced pyrimidine dimer photoproduct formation at multiple loci on the DNA indicative of changes in major groove architecture.

A non-invasive method for studying viral DNA delivery to bacteria reveals key requirements for phage SPP1 DNA entry in Bacillus subtilis cells

Bacteriophages use most frequently a tail apparatus to create a channel across the entire bacterial cell envelope to transfer the viral genome to the host cell cytoplasm, initiating infection. Characterization of this critical step remains a major challenge due to the difficulty to monitor DNA entry in the bacterium and its requirements. In this work we developed a new method to study phage DNA entry that has the potential to be extended to many tailed phages. Its application to study genome delivery of bacteriophage SPP1 into Bacillus subtilis disclosed a key role of the host cell membrane potential in the DNA entry process. An energized B. subtilis membrane and a millimolar concentration of calcium ions are shown to be major requirements for SPP1 DNA entry following the irreversible binding of phage particles to the receptor YueB.

Can Changes in Temperature or Ionic Conditions Modify the DNA Organization in the Full Bacteriophage Capsid?

We compared four bacteriophage species, T5, λ, T7, and Φ29, to explore the possibilities of DNA reorganization in the capsid where the chain is highly concentrated and confined. First, we did not detect any change in DNA organization as a function of temperature between 20 to 40 °C. Second, the presence of spermine (4+) induces a significant enlargement of the typical size of the hexagonal domains in all phages. We interpret these changes as a reorganization of DNA by slight movements of defects in the structure, triggered by a partial screening of repulsive interactions. We did not detect any signal characteristic of a long-range chiral organization of the encapsidated DNA in the presence and in the absence of spermine.

Clusters of polyhedra in spherical confinement

Dense particle packing in a confining volume remains a rich, largely unexplored problem, despite applications in blood clotting, plasmonics, industrial packaging and transport, colloidal molecule design, and information storage. Here, we report densest found clusters of the Platonic solids in spherical confinement, for up to [Formula: see text] constituent polyhedral particles. We examine the interplay between anisotropic particle shape and isotropic 3D confinement. Densest clusters exhibit a wide variety of symmetry point groups and form in up to three layers at higher N. For many N values, icosahedra and dodecahedra form clusters that resemble sphere clusters. These common structures are layers of optimal spherical codes in most cases, a surprising fact given the significant faceting of the icosahedron and dodecahedron. We also investigate cluster density as a function of N for each particle shape. We find that, in contrast to what happens in bulk, polyhedra often pack less densely than spheres. We also find especially dense clusters at so-called magic numbers of constituent particles. Our results showcase the structural diversity and experimental utility of families of solutions to the packing in confinement problem.

Coexistence of coil and globule domains within a single confined DNA chain

The highly charged DNA chain may be either in an extended conformation, the coil, or condensed into a highly dense and ordered structure, the toroid. The transition, also called collapse of the chain, can be triggered in different ways, for example by changing the ionic conditions of the solution. We observe individual DNA molecules one by one, kept separated and confined inside a protein shell (the envelope of a bacterial virus, 80 nm in diameter). For subcritical concentrations of spermine (4+), part of the DNA is condensed and organized in a toroid and the other part of the chain remains uncondensed around. Two states coexist along the same DNA chain. These ‘hairy’ globules are imaged by cryo-electron microscopy. We describe the global conformation of the chain and the local ordering of DNA segments inside the toroid.

Ionic switch controls the DNA state in phage λ

We have recently found that DNA packaged in phage λ undergoes a disordering transition triggered by temperature, which results in increased genome mobility. This solid-to-fluid like DNA transition markedly increases the number of infectious λ particles facilitating infection. However, the structural transition strongly depends on temperature and ionic conditions in the surrounding medium. Using titration microcalorimetry combined with solution X-ray scattering, we mapped both energetic and structural changes associated with transition of the encapsidated λ-DNA. Packaged DNA needs to reach a critical stress level in order for transition to occur. We varied the stress on DNA in the capsid by changing the temperature, packaged DNA length and ionic conditions. We found striking evidence that the intracapsid DNA transition is 'switched on' at the ionic conditions mimicking those in vivo and also at the physiologic temperature of infection at 37°C. This ion regulated on-off switch of packaged DNA mobility in turn affects viral replication. These results suggest a remarkable adaptation of phage λ to the environment of its host bacteria in the human gut. The metastable DNA state in the capsid provides a new paradigm for the physical evolution of viruses.

Modeling Viral Capsid Assembly

I present a review of the theoretical and computational methodologies that have been used to model the assembly of viral capsids. I discuss the capabilities and limitations of approaches ranging from equilibrium continuum theories to molecular dynamics simulations, and I give an overview of some of the important conclusions about virus assembly that have resulted from these modeling efforts. Topics include the assembly of empty viral shells, assembly around single-stranded nucleic acids to form viral particles, and assembly around synthetic polymers or charged nanoparticles for nanotechnology or biomedical applications. I present some examples in which modeling efforts have promoted experimental breakthroughs, as well as directions in which the connection between modeling and experiment can be strengthened.

Continuity of states between the cholesteric → line hexatic transition and the condensation transition in DNA solutions

A new method of finely temperature-tuning osmotic pressure allows one to identify the cholesteric → line hexatic transition of oriented or unoriented long-fragment DNA bundles in monovalent salt solutions as first order, with a small but finite volume discontinuity. This transition is similar to the osmotic pressure-induced expanded → condensed DNA transition in polyvalent salt solutions at small enough polyvalent salt concentrations. Therefore there exists a continuity of states between the two. This finding, together with the corresponding empirical equation of state, effectively relates the phase diagram of DNA solutions for monovalent salts to that for polyvalent salts and sheds some light on the complicated interactions between DNA molecules at high densities.

Solid-to-fluid-like DNA transition in viruses facilitates infection

Releasing the packaged viral DNA into the host cell is an essential process to initiate viral infection. In many double-stranded DNA bacterial viruses and herpesviruses, the tightly packaged genome is hexagonally ordered and stressed in the protein shell, called the capsid. DNA condensed in this state inside viral capsids has been shown to be trapped in a glassy state, with restricted molecular motion in vitro. This limited intracapsid DNA mobility is caused by the sliding friction between closely packaged DNA strands, as a result of the repulsive interactions between the negative charges on the DNA helices. It had been unclear how this rigid crystalline structure of the viral genome rapidly ejects from the capsid, reaching rates of 60,000 bp/s. Through a combination of single-molecule and bulk techniques, we determined how the structure and energy of the encapsidated DNA in phage λ regulates the mobility required for its ejection. Our data show that packaged λ-DNA undergoes a solid-to-fluid-like disordering transition as a function of temperature, resulting locally in less densely packed DNA, reducing DNA-DNA repulsions. This process leads to a significant increase in genome mobility or fluidity, which facilitates genome release at temperatures close to that of viral infection (37 °C), suggesting a remarkable physical adaptation of bacterial viruses to the environment of Escherichia coli cells in a human host.

Nonequilibrium dynamics and ultraslow relaxation of confined DNA during viral packaging

Many viruses use molecular motors that generate large forces to package DNA to near-crystalline densities inside preformed viral proheads. Besides being a key step in viral assembly, this process is of interest as a model for understanding the physics of charged polymers under tight 3D confinement. A large number of theoretical studies have modeled DNA packaging, and the nature of the molecular dynamics and the forces resisting the tight confinement is a subject of wide debate. Here, we directly measure the packaging of single DNA molecules in bacteriophage phi29 with optical tweezers. Using a new technique in which we stall the motor and restart it after increasing waiting periods, we show that the DNA undergoes nonequilibrium conformational dynamics during packaging. We show that the relaxation time of the confined DNA is >10 min, which is longer than the time to package the viral genome and 60,000 times longer than that of the unconfined DNA in solution. Thus, the confined DNA molecule becomes kinetically constrained on the timescale of packaging, exhibiting glassy dynamics, which slows the motor, causes significant heterogeneity in packaging rates of individual viruses, and explains the frequent pausing observed in DNA translocation. These results support several recent hypotheses proposed based on polymer dynamics simulations and show that packaging cannot be fully understood by quasistatic thermodynamic models.

Length quantization of DNA partially expelled from heads of a bacteriophage T3 mutant

DNA packaging of phages phi29, T3 and T7 sometimes produces incompletely packaged DNA with quantized lengths, based on gel electrophoretic band formation. We discover here a packaging ATPase-free, in vitro model for packaged DNA length quantization. We use directed evolution to isolate a five-site T3 point mutant that hyper-produces tail-free capsids with mature DNA (heads). Three tail gene mutations, but no head gene mutations, are present. A variable-length DNA segment leaks from some mutant heads, based on DNase I-protection assay and electron microscopy. The protected DNA segment has quantized lengths, based on restriction endonuclease analysis: six sharp bands of DNA missing 3.7-12.3% of the last end packaged. Native gel electrophoresis confirms quantized DNA expulsion and, after removal of external DNA, provides evidence that capsid radius is the quantization-ruler. Capsid-based DNA length quantization possibly evolved via selection for stalling that provides time for feedback control during DNA packaging and injection.

RELATIONSHIP BETWEEN THE GENOME PACKING IN THE BACTERIOPHAGE CAPSID AND THE KINETICS OF DNA EJECTION

We present a general survey of experimental and theoretical observations of DNA structure and in vitro ejection kinetics for different bacteriophage species. In some species, like T5, the ejection may present pauses and arrests that have not been detected in others species like Lambda. We propose hypotheses to explain such differences and we discuss how the experimental conditions may be important for their detection. Our work highlights the role of DNA organization inside the bacteriophage capsid on the stochastic and out of equilibrium nature of the ejection process.

Molecular architecture of tailed double-stranded DNA phages

The tailed double-stranded DNA bacteriophages, or Caudovirales, constitute ~96% of all the known phages. Although these phages come in a great variety of sizes and morphology, their virions are mainly constructed of similar molecular building blocks via similar assembly pathways. Here we review the structure of tailed double-stranded DNA bacteriophages at a molecular level, emphasizing the structural similarity and common evolutionary origin of proteins that constitute these virions.

Langevin dynamics simulation of DNA ejection from a phage

We have performed Langevin dynamics simulations of a coarse-grained model of ejection of dsDNA from Φ29 phage. Our simulation results show significant variations in the local ejection speed, consistent with experimental observations reported in the literature for both in vivo and in vitro systems. In efforts to understand the origin of such variations in the local speed of ejection, we have investigated the correlations between the local ejection kinetics and the packaged structures created at various motor forces and chain flexibility. At lower motor forces, the packaged DNA length is shorter with better organization. On the other hand, at higher motor forces typical of realistic situations, the DNA organization inside the capsid suffers from significant orientational disorder, but yet with long orientational correlation times. This in turn leads to lack of registry between the direction of the DNA segments just to be ejected and the direction of exit. As a result, a significant amount of momentum transfer is required locally for successful exit. Consequently, the DNA ejection temporarily slows down exhibiting pauses. This slowing down occurs at random times during the ejection process, completely determined by the particular starting conformation created by prescribed motor forces. In order to augment our inference, we have additionally investigated the ejection of chains with deliberately changed persistence length. For less inflexible chains, the demand on the occurrence of large momentum transfer for successful ejection is weaker, resulting in more uniform ejection kinetics. While being consistent with experimental observations, our results show the nonergodic nature of the ejection kinetics and call for better theoretical models to portray the kinetics of genome ejection from phages.

Polymorphism of DNA conformation inside the bacteriophage capsid

Double-stranded DNA bacteriophage genomes are packaged into their icosahedral capsids at the highest densities known so far (about 50 % w:v). How the molecule is folded at such density and how its conformation changes upon ejection or packaging are fascinating questions still largely open. We review cryo-TEM analyses of DNA conformation inside partially filled capsids as a function of the physico-chemical environment (ions, osmotic pressure, temperature). We show that there exists a wide variety of DNA conformations. Strikingly, the different observed structures can be described by some of the different models proposed over the years for DNA organisation inside bacteriophage capsids: either spool-like structures with axial or concentric symmetries, or liquid crystalline structures characterised by a DNA homogeneous density. The relevance of these conformations for the understanding of DNA folding and unfolding upon ejection and packaging in vivo is discussed.

Popping the cork: mechanisms of phage genome ejection

Sixty years after Hershey and Chase showed that nucleic acid is the major component of phage particles that is ejected into cells, we still do not fully understand how the process occurs. Advances in electron microscopy have revealed the structure of the condensed DNA confined in a phage capsid, and the mechanisms and energetics of packaging a phage genome are beginning to be better understood. Condensing DNA subjects it to high osmotic pressure, which has been suggested to provide the driving force for its ejection during infection. However, forces internal to a phage capsid cannot, alone, cause complete genome ejection into cells. Here, we describe the structure of the DNA inside mature phages and summarize the current models of genome ejection, both in vitro and in vivo.

Role of osmotic and hydrostatic pressures in bacteriophage genome ejection

A critical step in the bacteriophage life cycle is genome ejection into host bacteria. The ejection process for double-stranded DNA phages has been studied thoroughly in vitro, where after triggering with the cellular receptor the genome ejects into a buffer. The experimental data have been interpreted in terms of the decrease in free energy of the densely packed DNA associated with genome ejection. Here we detail a simple model of genome ejection in terms of the hydrostatic and osmotic pressures inside the phage, a bacterium, and a buffer solution or culture medium. We argue that the hydrodynamic flow associated with the water movement from the buffer solution into the phage capsid and further drainage into the bacterial cytoplasm, driven by the osmotic gradient between the bacterial cytoplasm and culture medium, provides an alternative mechanism for phage genome ejection in vivo; the mechanism is perfectly consistent with phage genome ejection in vitro.

Probing the elasticity of DNA on short length scales by modeling supercoiling under tension

The wormlike-chain (WLC) model is widely used to describe the energetics of DNA bending. Motivated by recent experiments, alternative, so-called subelastic chain models were proposed that predict a lower elastic energy of highly bent DNA conformations. Until now, no unambiguous verification of these models has been obtained because probing the elasticity of DNA on short length scales remains challenging. Here we investigate the limits of the WLC model using coarse-grained Monte Carlo simulations to model the supercoiling of linear DNA molecules under tension. At a critical supercoiling density, the DNA extension decreases abruptly due to the sudden formation of a plectonemic structure. This buckling transition is caused by the large energy required to form the tightly bent end-loop of the plectoneme and should therefore provide a sensitive benchmark for model evaluation. Although simulations based on the WLC energetics could quantitatively reproduce the buckling measured in magnetic tweezers experiments, the buckling almost disappears for the tested linear subelastic chain model. Thus, our data support the validity of a harmonic bending potential even for small bending radii down to 3.5 nm.

Capsid structure and its stability at the late stages of bacteriophage SPP1 assembly

The structure of the bacteriophage SPP1 capsid was determined at subnanometer resolution by cryo-electron microscopy and single-particle analysis. The icosahedral capsid is composed of the major capsid protein gp13 and the auxiliary protein gp12, which are organized in a T=7 lattice. DNA is arranged in layers with a distance of ~24.5 Å. gp12 forms spikes that are anchored at the center of gp13 hexamers. In a gp12-deficient mutant, the centers of hexamers are closed by loops of gp13 coming together to protect the SPP1 genome from the outside environment. The HK97-like fold was used to build a pseudoatomic model of gp13. Its structural organization remains unchanged upon tail binding and following DNA release. gp13 exhibits enhanced thermostability in the DNA-filled capsid. A remarkable convergence between the thermostability of the capsid and those of the other virion components was found, revealing that the overall architecture of the SPP1 infectious particle coevolved toward high robustness.

Condensed genome structure

Large, tailed dsDNA-containing bacteriophage genomes are packaged to a conserved and high density (∼500 mg/ml), generally in ∼2.5-nm, duplex-to-duplex, spaced, organized DNA shells within icosahedral capsids. Phages with these condensate properties, however, differ markedly in their inner capsid structures: (1) those with a naked condensed DNA, (2) those with many dispersed unstructured proteins embedded within the DNA, (3) those with a small number of localized proteins, and (4) those with a reduced or DNA-free internal protein structure of substantial volume. The DNA is translocated and condensed by a high-force ATPase motor into a procapsid already containing the proteins that are to be ejected together with the DNA into the infected host. The condensed genome structure of a single-phage type is unlikely to be precisely determined and can change without loss of function to fit an altered capsid size or internal structure. Although no such single-phage condensed genome structure is known exactly, it is known that a single general structure is unlikely to apply to all such phages.

Short noncontractile tail machines: adsorption and DNA delivery by podoviruses

Tailed dsDNA bacteriophage virions bind to susceptible cells with the tips of their tails and then deliver their DNA through the tail into the cells to initiate infection. This chapter discusses what is known about this process in the short-tailed phages (Podoviridae). Their short tails require that many of these virions adsorb to the outer layers of the cell and work their way down to the outer membrane surface before releasing their DNA. Interestingly, the receptor-binding protein of many short-tailed phages (and some with long tails) has an enzymatic activity that cleaves their polysaccharide receptors. Reversible adsorption and irreversible adsorption to primary and secondary receptors are discussed, including how sequence divergence in tail fiber and tailspike proteins leads to different host specificities. Upon reaching the outer membrane of Gram-negative cells, some podoviral tail machines release virion proteins into the cell that help the DNA efficiently traverse the outer layers of the cell and/or prepare the cell cytoplasm for phage genome arrival. Podoviruses utilize several rather different variations on this theme. The virion DNA is then released into the cell; the energetics of this process is discussed. Phages like T7 and N4 deliver their DNA relatively slowly, using enzymes to pull the genome into the cell. At least in part this mechanism ensures that genes in late-entering DNA are not expressed at early times. On the other hand, phages like P22 probably deliver their DNA more rapidly so that it can be circularized before the cascade of gene expression begins.

A PHYLLOTACTIC APPROACH TO THE STRUCTURE OF COLLAGEN FIBRILS

Collagen fibrils, cable-like assemblies of long biological molecules, the so-called triple helices, are dominant components of connective tissues. Their determinant morphological and functional roles motivated a large number of studies concerning their formation and structure. However, these two points are still open questions and, particularly, that of the lateral assembly of the triple helices which is certainly dense but not strictly that of a well-ordered molecular crystal. We examine here the geometrical template provided by the algorithm of phyllotaxis which gives to each element of an assembly of points or parallel rods the most homogeneous and isotropic dense environment in a situation of cylindrical symmetry. The scattered intensity obtained from a phyllotactic distribution of triple helices in collagen fibrils presents features which could contribute to the scattering observed along the equatorial direction of their X-ray patterns. Following this approach, the aggregation of triple helices in fibrils should be considered within the frame of soft condensed matter studies rather than that of molecular crystal studies.

Protein-DNA interactions determine the shapes of DNA toroids condensed in virus capsids

DNA toroids that form inside the bacteriophage capsid present different shapes according to whether they are formed by the addition of spermine or polyethylene glycol to the bathing solution. Spermine-DNA toroids present a convex, faceted section with no or minor distortions of the DNA interstrand spacing with respect to those observed in the bulk, whereas polyethylene glycol-induced toroids are flattened to the capsid inner surface and show a crescent-like, nonconvex shape. By modeling the energetics of the DNA toroid using a free-energy functional composed of energy contributions related to the elasticity of the wound DNA, exposed surface DNA energy, and adhesion between the DNA and the capsid, we established that the crescent shape of the toroidal DNA section comes from attractive interactions between DNA and the capsid. Such attractive interactions seem to be specific to the PEG condensation process and are not observed in the case of spermine-induced DNA condensation.