Spindle-shaped archaeal viruses evolved from rod-shaped ancestors to package a larger genome.

Spindle- or lemon-shaped viruses infect archaea in diverse environments. Due to the highly pleomorphic nature of these virions, which can be found with cylindrical tails emanating from the spindle-shaped body, structural studies of these capsids have been challenging. We have determined the atomic structure of the capsid of Sulfolobus monocaudavirus 1, a virus that infects hosts living in nearly boiling acid. A highly hydrophobic protein, likely integrated into the host membrane before the virions assemble, forms 7 strands that slide past each other in both the tails and the spindle body. We observe the discrete steps that occur as the tail tubes expand, and these are due to highly conserved quasiequivalent interactions with neighboring subunits maintained despite significant diameter changes. Our results show how helical assemblies can vary their diameters, becoming nearly spherical to package a larger genome and suggest how all spindle-shaped viruses have evolved from archaeal rod-like viruses.

Toxic PR Poly-Dipeptides Encoded by the C9orf72 Repeat Expansion Target LC Domain Polymers.

Two complementary approaches were used in search of the intracellular targets of the toxic PR poly-dipeptide encoded by the repeat sequences expanded in the C9orf72 form of amyotrophic lateral sclerosis. The top categories of PRn-bound proteins include constituents of non-membrane invested cellular organelles and intermediate filaments. PRn targets are enriched for the inclusion of low complexity (LC) sequences. Evidence is presented indicating that LC sequences represent the direct target of PRn binding and that interaction between the PRn poly-dipeptide and LC domains is polymer-dependent. These studies indicate that PRn-mediated toxicity may result from broad impediments to the dynamics of cell structure and information flow from gene to message to protein.

The 3D Genome as Moderator of Chromosomal Communication.

Proper expression of genes requires communication with their regulatory elements that can be located elsewhere along the chromosome. The physics of chromatin fibers imposes a range of constraints on such communication. The molecular and biophysical mechanisms by which chromosomal communication is established, or prevented, have become a topic of intense study, and important roles for the spatial organization of chromosomes are being discovered. Here we present a view of the interphase 3D genome characterized by extensive physical compartmentalization and insulation on the one hand and facilitated long-range interactions on the other. We propose the existence of topological machines dedicated to set up and to exploit a 3D genome organization to both promote and censor communication along and between chromosomes.

A conceptual framework for understanding phase separation and addressing open questions and challenges.

Macromolecular phase separation is being recognized for its potential importance and relevance as a driver of spatial organization within cells. Here, we describe a framework based on synergies between networking (percolation or gelation) and density (phase separation) transitions. Accordingly, the phase transitions in question are referred to as phase separation coupled to percolation (PSCP). The condensates that result from PSCP are viscoelastic network fluids. Such systems have sequence-, composition-, and topology-specific internal network structures that give rise to time-dependent interplays between viscous and elastic properties. Unlike pure phase separation, the process of PSCP gives rise to sequence-, chemistry-, and structure-specific distributions of clusters that can form at concentrations that lie well below the threshold concentration for phase separation. PSCP, influenced by specific versus solubility-determining interactions, also provides a bridge between different observations and helps answer questions and address challenges that have arisen regarding the role of macromolecular phase separation in biology.

Rubber-glass nanocomposites fabricated using mixed emulsions.

Many composites consist of matrices of elastomers and nanoparticles of stiff materials. Such composites often have superior properties and are widely used. Embedding elastomers with nanoparticles commonly necessitates intense shear, using machines like extruders and roll millers, which cut polymer chains and degrade properties. Here, we prepare a rubber-glass nanocomposite by using two aqueous emulsions. Each emulsion is separately prepared with a single species of polymer chains. Each polymer chain is copolymerized with a small amount of silane coupling agent. Upon mixing the two emulsions, as water evaporates, the glassy particles retain the shape, and the rubbery particles change shape to form a continuous matrix. Subsequently, the silane coupling agent condensates, which cross-links the rubbery chains and interlinks the rubbery chains to the glassy particles. The cross-links and interlinks stabilize the nanostructure and lead to superior properties. The nanocomposite simultaneously achieves high modulus (~30 MPa), high toughness (~100 kJ m-2), and high fatigue threshold (~1,000 J m-2). The method of mixed emulsion is environmentally friendly and compatible with various open-air manufacturing processes, such as coat, cast, spray, print, and brush. Additionally, the silane coupling agent can interlink the nanocomposite to other materials. The method of mixed emulsion can be used to fabricate objects of complex shapes, fine features, and prescribed spatial variations of compositions.

3D observations provide striking findings in rubber elasticity.

The mechanical response of rubbers has been ubiquitously assumed to be only a function of the imposed strain. Using innovative X-ray measurements capturing the three-dimensional spatial volumetric strain fields, we demonstrate that rubbers and indeed many common engineering polymers undergo significant local volume changes. But remarkably, the overall specimen volume remains constant regardless of the imposed loading. This strange behavior which also leads to apparent negative local bulk moduli is due to the presence of a mobile phase within these materials. Combining X-ray tomographic observations with high-speed radiography to track the motion of the mobile phase, we have revised classical thermodynamic frameworks of rubber elasticity. The work opens broad avenues to understand not only the mechanical behavior of rubbers but a large class of widely used engineering polymers.

Unified understanding of the impact of semiflexibility, concentration, and molecular weight on macromolecular-scale ring diffusion.

Conformationally fluctuating, globally compact macromolecules such as polymeric rings, single-chain nanoparticles, microgels, and many-arm stars display complex dynamic behaviors due to their rich topological structure and intermolecular organization. Synthetic rings are hybrid objects with conformations that display both ideal random walk and compact globular features, which can serve as models of genomic DNA. To date, emphasis has been placed on the effect of ring molecular weight on their unusual behaviors. Here, we combine simulations and a microscopic force-level theory to build a unified understanding for how key aspects of ring dynamics depend on different tunable molecular properties including backbone rigidity, monomer concentration, degree of traditional entanglement, and molecular weight. Our large-scale molecular dynamics simulations of ring melts with very different backbone stiffnesses reveal unanticipated behaviors which agree well with our generalized theory. This includes a universal master curve for center-of-mass diffusion constants as a function of molecular weight scaled by a chemistry and thermodynamic state-dependent critical molecular weight that generalizes the concept of an entanglement cross-over for linear chains. The key physics is how backbone rigidity and monomer concentration induced changes of the entanglement length, interring packing, degree of interpenetration, and liquid compressibility slow down space-time dynamic-force correlations on macromolecular scales. A power law decay of the center-of-mass diffusion constant with inverse molecular weight squared is the first consequence, followed by an ultraslow activated hopping transport regime. Our results set the stage to address slow dynamics and kinetic arrest in different families of compact synthetic and biological polymeric systems.

Ring-opening metathesis polymerization of N-methylpyridinium-fused norbornenes to access antibacterial main-chain cationic polymers.

Cationic polymers have been identified as a promising type of antibacterial molecules, whose bioactivity can be tuned through structural modulation. Recent studies suggest that the placement of the cationic groups close to the core of the polymeric architecture rather than on appended side chains might improve both their bioactivity and selectivity for bacterial cells over mammalian cells. However, antibacterial main-chain cationic polymers are typically synthesized via polycondensations, which do not afford precise and uniform molecular design. Therefore, accessing main-chain cationic polymers with high degrees of molecular tunability hinges upon the development of controlled polymerizations tolerating cationic motifs (or cation progenitors) near the propagating species. Herein, we report the synthesis and ring-opening metathesis polymerization (ROMP) of N-methylpyridinium-fused norbornene monomers. The identification of reaction conditions leading to a well-controlled ROMP enabled structural diversification of the main-chain cationic polymers and a study of their bioactivity. This family of polyelectrolytes was found to be active against both Gram-negative (Escherichia coli) and Gram-positive (Methicillin-resistant Staphylococcus aureus) bacteria with minimal inhibitory concentrations as low as 25 µg/mL. Additionally, the molar mass of the polymers was found to impact their hemolytic activity with cationic polymers of smaller degrees of polymerization showing increased selectivity for bacteria over human red blood cells.

Tad and toxin-coregulated pilus structures reveal unexpected diversity in bacterial type IV pili.

Type IV pili (T4P) are ubiquitous in both bacteria and archaea. They are polymers of the major pilin protein, which has an extended and protruding N-terminal helix, α1, and a globular C-terminal domain. Cryo-EM structures have revealed key differences between the bacterial and archaeal T4P in their C-terminal domain structure and in the packing and continuity of α1. This segment forms a continuous α-helix in archaeal T4P but is partially melted in all published bacterial T4P structures due to a conserved helix breaking proline at position 22. The tad (tight adhesion) T4P are found in both bacteria and archaea and are thought to have been acquired by bacteria through horizontal transfer from archaea. Tad pilins are unique among the T4 pilins, being only 40 to 60 residues in length and entirely lacking a C-terminal domain. They also lack the Pro22 found in all high-resolution bacterial T4P structures. We show using cryo-EM that the bacterial tad pilus from Caulobacter crescentus is composed of continuous helical subunits that, like the archaeal pilins, lack the melted portion seen in other bacterial T4P and share the packing arrangement of the archaeal T4P. We further show that a bacterial T4P, the Vibrio cholerae toxin coregulated pilus, which lacks Pro22 but is not in the tad family, has a continuous N-terminal α-helix, yet its α1 s are arranged similar to those in other bacterial T4P. Our results highlight the role of Pro22 in helix melting and support an evolutionary relationship between tad and archaeal T4P.

The evolution of archaeal flagellar filaments.

Flagellar motility has independently arisen three times during evolution: in bacteria, archaea, and eukaryotes. In prokaryotes, the supercoiled flagellar filaments are composed largely of a single protein, bacterial or archaeal flagellin, although these two proteins are not homologous, while in eukaryotes, the flagellum contains hundreds of proteins. Archaeal flagellin and archaeal type IV pilin are homologous, but how archaeal flagellar filaments (AFFs) and archaeal type IV pili (AT4Ps) diverged is not understood, in part, due to the paucity of structures for AFFs and AT4Ps. Despite having similar structures, AFFs supercoil, while AT4Ps do not, and supercoiling is essential for the function of AFFs. We used cryo-electron microscopy to determine the atomic structure of two additional AT4Ps and reanalyzed previous structures. We find that all AFFs have a prominent 10-strand packing, while AT4Ps show a striking structural diversity in their subunit packing. A clear distinction between all AFF and all AT4P structures involves the extension of the N-terminal α-helix with polar residues in the AFFs. Additionally, we characterize a flagellar-like AT4P from Pyrobaculum calidifontis with filament and subunit structure similar to that of AFFs which can be viewed as an evolutionary link, showing how the structural diversity of AT4Ps likely allowed for an AT4P to evolve into a supercoiling AFF.

Flexible fluid-based encapsulation platform for water-sensitive materials.

The next-generation semiconductors and devices, such as halide perovskites and flexible electronics, are extremely sensitive to water, thus demanding highly effective protection that not only seals out water in all forms (vapor, droplet, and ice), but simultaneously provides mechanical flexibility, durability, transparency, and self-cleaning. Although various solid-state encapsulation methods have been developed, no strategy is available that can fully meet all the above requirements. Here, we report a bioinspired liquid-based encapsulation strategy that offers protection from water without sacrificing the operational properties of the encapsulated materials. Using halide perovskite as a model system, we show that damage to the perovskite from exposure to water is drastically reduced when it is coated by a polymer matrix with infused hydrophobic oil. With a combination of experimental and simulation studies, we elucidated the fundamental transport mechanisms of ultralow water transmission rate that stem from the ability of the infused liquid to fill-in and reduce defects in the coating layer, thus eliminating the low-energy diffusion pathways, and to cause water molecules to diffuse as clusters, which act together as an excellent water permeation barrier. Importantly, the presence of the liquid, as the central component in this encapsulation method provides a unique possibility of reversing the water transport direction; therefore, the lifetime of enclosed water-sensitive materials could be significantly extended via replenishing the hydrophobic oils regularly. We show that the liquid encapsulation platform presented here has high potential in providing not only water protection of the functional device but also flexibility, optical transparency, and self-healing of the coating layer, which are critical for a variety of applications, such as in perovskite solar cells and bioelectronics.

High-throughput experimentation for discovery of biodegradable polyesters.

The consistent rise of plastic pollution has stimulated interest in the development of biodegradable plastics. However, the study of polymer biodegradation has historically been limited to a small number of polymers due to costly and slow standard methods for measuring degradation, slowing new material innovation. High-throughput polymer synthesis and a high-throughput polymer biodegradation method are developed and applied to generate a biodegradation dataset for 642 chemically distinct polyesters and polycarbonates. The biodegradation assay was based on the clear-zone technique, using automation to optically observe the degradation of suspended polymer particles under the action of a single Pseudomonas lemoignei bacterial colony. Biodegradability was found to depend strongly on aliphatic repeat unit length, with chains less than 15 carbons and short side chains improving biodegradability. Aromatic backbone groups were generally detrimental to biodegradability; however, ortho- and para-substituted benzene rings in the backbone were more likely to be degradable than metasubstituted rings. Additionally, backbone ether groups improved biodegradability. While other heteroatoms did not show a clear improvement in biodegradability, they did demonstrate increases in biodegradation rates. Machine learning (ML) models were leveraged to predict biodegradability on this large dataset with accuracies over 82% using only chemical structure descriptors.

How entanglements determine the morphology of semicrystalline polymers.

Crystallization of polymers from entangled melts generally leads to the formation of semicrystalline materials with a nanoscopic morphology consisting of stacks of alternating crystalline and amorphous layers. The factors controlling the thickness of the crystalline layers are well studied; however, there is no quantitative understanding of the thickness of the amorphous layers. We elucidate the effect of entanglements on the semicrystalline morphology by the use of a series of model blends of high-molecular-weight polymers with unentangled oligomers leading to a reduced entanglement density in the melt as characterized by rheological measurements. Small-angle X-ray scattering experiments after isothermal crystallization reveal a reduced thickness of the amorphous layers, while the crystal thickness remains largely unaffected. We introduce a simple, yet quantitative model without adjustable parameters, according to which the measured thickness of the amorphous layers adjusts itself in such a way that the entanglement concentration reaches a specific maximum value. Furthermore, our model suggests an explanation for the large supercooling that is typically required for crystallization of polymers if entanglements cannot be dissolved during crystallization.

Controlling swelling in mixed transport polymers through alkyl side-chain physical cross-linking.

Semiconducting conjugated polymers bearing glycol side chains can simultaneously transport both electronic and ionic charges with high charge mobilities, making them ideal electrode materials for a range of bioelectronic devices. However, heavily glycolated conjugated polymer films have been observed to swell irreversibly when subjected to an electrochemical bias in an aqueous electrolyte. The excessive swelling can lead to the degradation of their microstructure, and subsequently reduced device performance. An effective strategy to control polymer film swelling is to copolymerize glycolated repeat units with a fraction of monomers bearing alkyl side chains, although the microscopic mechanism that constrains swelling is unknown. Here we investigate, experimentally and computationally, a series of archetypal mixed transporting copolymers with varying ratios of glycolated and alkylated repeat units. Experimentally we observe that exchanging 10% of the glycol side chains for alkyl leads to significantly reduced film swelling and an increase in electrochemical stability. Through molecular dynamics simulation of the amorphous phase of the materials, we observe the formation of polymer networks mediated by alkyl side-chain interactions. When in the presence of water, the network becomes increasingly connected, counteracting the volumetric expansion of the polymer film.

Anomalous magnetoresistance in a nonconjugated radical polymer glass.

Macromolecules bearing open-shell entities offer unique transport properties for both electronic and spintronic devices. This work demonstrates that, unlike their conjugated polymer counterparts, the charge carriers in radical polymers (i.e., macromolecules with nonconjugated backbones and with stable open-shell sites present at their pendant groups) are singlet cations, which opens significant avenues for manipulating macromolecular design for advanced solid-state transport in these highly transparent conductors. Despite this key point, magnetoresistive effects are present in radical polymer thin films under applied magnetic fields due to the presence of impurity sites in low (i.e., <1%) concentrations. Additionally, thermal annealing of poly(4-glycidyloxy-2,2,6,6- tetramethylpiperidine-1-oxyl) (PTEO), a nonconjugated polymer with stable open-shell pendant groups, facilitated better electron exchange and pairwise spin interactions resulting in an unexpected magnetoresistance signal at relatively low field strengths (i.e., <2 T). The addition of 4-hydroxy-2,2,6,6-tetramethylpiperidin-N-oxy (TEMPO-OH), a paramagnetic species, increased the magnitude of the MR effect when the small molecule was added to the radical polymer matrix. These macroscopic experimental observables are explained using computational approaches that detail the fundamental molecular principles. This intrinsic localized charge transport behavior differs from the current state of the art regarding closed-shell conjugated macromolecules, and it opens an avenue towards next-generation transport in organic electronic materials.

Harnessing Immunomodulatory Polymers for Treatment of Autoimmunity, Allergy, and Transplant Rejection.

Autoimmunity, allergy, and transplant rejection are a collection of chronic diseases that are currently incurable, drastically decrease patient quality of life, and consume considerable health care resources. Underlying each of these diseases is a dysregulated immune system that results in the mounting of an inflammatory response against self or an innocuous antigen. As a consequence, afflicted patients are required to adhere to lifelong regimens of multiple immunomodulatory drugs to control disease and reclaim agency. Unfortunately, current immunomodulatory drugs are associated with a myriad of side effects and adverse events, such as increased risk of cancer and increased risk of serious infection, which negatively impacts patient adherence rates and quality of life. The field of immunoengineering is a new discipline that aims to harness endogenous biological pathways to thwart disease and minimize side effects using novel biomaterial-based strategies. We highlight and discuss polymeric micro/nanoparticles with inherent immunomodulatory properties that are currently under investigation in biomaterial-based therapies for treatment of autoimmunity, allergy, and transplant rejection.

Mass spectrometry of polymers: A tutorial review.

Ever since the inception of synthetic polymeric materials in the late 19th century, the number of studies on polymers as well as the complexity of their structures have only increased. The development and commercialization of new polymers with properties fine-tuned for specific technological, environmental, consumer, or biomedical applications requires powerful analytical techniques that permit the in-depth characterization of these materials. One such method with the ability to provide chemical composition and structure information with high sensitivity, selectivity, specificity, and speed is mass spectrometry (MS). This tutorial review presents and exemplifies the various MS techniques available for the elucidation of specific structural features in a synthetic polymer, including compositional complexity, primary structure, architecture, topology, and surface properties. Key to every MS analysis is sample conversion to gas-phase ions. This review describes the fundamentals of the most suitable ionization methods for synthetic materials and provides relevant sample preparation protocols. Most importantly, structural characterizations via one-step as well as hyphenated or multidimensional approaches are introduced and demonstrated with specific applications, including surface sensitive and imaging techniques. The aim of this tutorial review is to illustrate the capabilities of MS for the characterization of large, complex polymers and emphasize its potential as a powerful compositional and structural elucidation tool in polymer chemistry.

Local Cancer Recurrence: The Realities, Challenges, and Opportunities for New Therapies.

Locoregional recurrence negatively impacts both long-term survival and quality of life for several malignancies. For appropriate-risk patients with an isolated, resectable, local recurrence, surgery represents the only potentially curative therapy. However, oncologic outcomes remain inferior for patients with locally recurrent disease even after macroscopically complete resection. Unfortunately, these operations are often extensive, with significant perioperative morbidity and mortality. This review highlights selected malignancies (mesothelioma, sarcoma, lung cancer, breast cancer, rectal cancer, and peritoneal surface malignancies) in which surgical resection is a key treatment modality and local recurrence plays a significant role in overall oncologic outcome with regard to survival and quality of life. For each type of cancer, the current, state-of-the-art treatment strategies and their outcomes are assessed. The need for additional therapeutic options is presented given the limitations of the current standard therapies. New and emerging treatment modalities, including polymer films and nanoparticles, are highlighted as potential future solutions for both prevention and treatment of locally recurrent cancers. Finally, the authors identify additional clinical and research opportunities and propose future research strategies based on the various patterns of local recurrence among the different cancers.

Exploring GPCR conformational dynamics using single-molecule fluorescence.

G protein-coupled receptors (GPCRs) are membrane proteins that transmit specific external stimuli into cells by changing their conformation. This conformational change allows them to couple and activate G-proteins to initiate signal transduction. A critical challenge in studying and inferring these structural dynamics arises from the complexity of the cellular environment, including the presence of various endogenous factors. Due to the recent advances in cell-expression systems, membrane-protein purification techniques, and labeling approaches, it is now possible to study the structural dynamics of GPCRs at a single-molecule level both in vitro and in live cells. In this review, we discuss state-of-the-art techniques and strategies for expressing, purifying, and labeling GPCRs in the context of single-molecule research. We also highlight four recent studies that demonstrate the applications of single-molecule microscopy in revealing the dynamics of GPCRs. These techniques are also useful as complementary methods to verify the results obtained from other structural biology tools like cryo-electron microscopy and x-ray crystallography.

Using Carbohydrate-Based Polymers to Facilitate Testicular Regeneration.

Male infertility is a significant global issue affecting 60-80 million people, with 40%-50% of cases linked to male issues. Exposure to radiation, drugs, sickness, the environment, and oxidative stress may result in testicular degeneration. Carbohydrate-based polymers (CBPs) restore testis differentiation and downregulate apoptosis genes. CBP has biodegradability, low cost, and wide availability, but is at risk of contamination and variations. CBP shows promise in wound healing, but more research is required before implementation in healthcare. Herein, we discuss the recent advances in engineering applications of CBP employed as scaffolds, drug delivery systems, immunomodulation, and stem cell therapy for testicular regeneration. Moreover, we emphasize the promising challenges warranted for future perspectives.