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.

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.

Archaeal bundling pili of Pyrobaculum calidifontis reveal similarities between archaeal and bacterial biofilms.

While biofilms formed by bacteria have received great attention due to their importance in pathogenesis, much less research has been focused on the biofilms formed by archaea. It has been known that extracellular filaments in archaea, such as type IV pili, hami, and cannulae, play a part in the formation of archaeal biofilms. We have used cryo-electron microscopy to determine the atomic structure of a previously uncharacterized class of archaeal surface filaments from hyperthermophilic Pyrobaculum calidifontis. These filaments, which we call archaeal bundling pili (ABP), assemble into highly ordered bipolar bundles. The bipolar nature of these bundles most likely arises from the association of filaments from at least two different cells. The component protein, AbpA, shows homology, both at the sequence and structural level, to the bacterial protein TasA, a major component of the extracellular matrix in bacterial biofilms, contributing to biofilm stability. We show that AbpA forms very stable filaments in a manner similar to the donor-strand exchange of bacterial TasA fibers and chaperone-usher pathway pili where a ß-strand from one subunit is incorporated into a ß-sheet of the next subunit. Our results reveal likely mechanistic similarities and evolutionary connection between bacterial and archaeal biofilms, and suggest that there could be many other archaeal surface filaments that are as yet uncharacterized.

Atomic structure of Lanreotide nanotubes revealed by cryo-EM.

Functional and versatile nano- and microassemblies formed by biological molecules are found at all levels of life, from cell organelles to full organisms. Understanding the chemical and physicochemical determinants guiding the formation of these assemblies is crucial not only to understand the biological processes they carry out but also to mimic nature. Among the synthetic peptides forming well-defined nanostructures, the octapeptide Lanreotide has been considered one of the best characterized, in terms of both the atomic structure and its self-assembly process. In the present work, we determined the atomic structure of Lanreotide nanotubes at 2.5-Å resolution by cryoelectron microscopy (cryo-EM). Surprisingly, the asymmetric unit in the nanotube contains eight copies of the peptide, forming two tetramers. There are thus eight different environments for the peptide, and eight different conformations in the nanotube. The structure built from the cryo-EM map is strikingly different from the molecular model, largely based on X-ray fiber diffraction, proposed 20 y ago. Comparison of the nanotube with a crystal structure at 0.83-Å resolution of a Lanreotide derivative highlights the polymorphism for this peptide family. This work shows once again that higher-order assemblies formed by even well-characterized small peptides are very difficult to predict.

Single-crystal-to-single-crystal translation of a helical supramolecular polymer to a helical covalent polymer.

Polymers possessing helical conformation in the solid state are in high demand. We report a helical peptide-polymer via the topochemical ene-azide cycloaddition (TEAC) polymerization. The molecules of the designed Gly-Phe-based dipeptide, decorated with ene and azide, assemble in its crystals as ß-sheets and as supramolecular helices in two mutually perpendicular directions. While the NH…O H-bonding facilitates ß-sheet-like stacking along one direction, weak CH…N H-bonding between the azide-nitrogen and vinylic-hydrogen of molecules belonging to the adjacent stacks arranges them in a head-to-tail manner as supramolecular helices. In the crystal lattice, the azide and alkene of adjacent molecules in the supramolecular helix are suitably preorganized for their TEAC reaction. The dipeptide underwent regio- and stereospecific polymerization upon mild heating in a single-crystal-to-single-crystal fashion, yielding a triazoline-linked helical covalent polymer that could be characterized by single-crystal X-ray diffraction studies. Upon heating, the triazoline-linked polymer undergoes denitrogenation to aziridine-linked polymer, as evidenced by differential scanning calorimetry, thermogravimetric analysis, and solid-state NMR analyses.

Polymeric Cholesteric Superhelix Induced by Chiral Helical Polymer for Achieving Full-Color Circularly Polarized Room-Temperature Phosphorescence with Ultra-High Dissymmetry Factor.

Circularly polarized room-temperature phosphorescence (CPRTP) simultaneously featuring multiple colors and extremely high dissymmetry factor (glum) is crucial for increasing the complexity of optical characteristics and advancing further development, but such a type of CPRTP is still unprecedented. The present work develops an effective and universal strategy to achieve full-color CPRTP with ultra-high glum factors in a polymeric cholesteric superhelix network, which is constructed by cholesteric liquid crystal polymer and chiral helical polymer (CHP). Taking advantage of the high helical twisting power of CHP, the resulting polymeric cholesteric superhelix network exhibits remarkable optical activity. Significantly, by adopting a simple double-layered architectures consisting of the cholesteric superhelix film and phosphorescent films, blue-, green-, yellow-, and red-CPRTP emissions are successfully obtained, with maximum |glum| values up to 1.43, 1.39, 1.09 and 0.84, respectively. Further, a multilevel information encryption application is demonstrated based on the multidimensional optical characteristics of the full-color double-layered CPRTP architectures. This study offers new insights into fabricating polymeric cholesteric superhelix with considerable CPRTP performance in advanced photonic applications.

Size dependence of optical activities in helical polymers.

Chiroptical properties of helical polymers do not always align with the sum of the local contributions of their unit cells. This study investigates the discrepancy in optical rotatory strength between local and global structures using a right-handed helical polyacetylene model. The chirality is examined through density functional theory (DFT) calculations. The analysis reveals that, at higher degrees of polymerization, the contribution of chirality from the helical strand generally surpasses the partial chirality from the local structure. The ratio of local contribution to total contribution is deduced within the framework of crystal orbital theory, and a numerical method using Wannier functions is presented for evaluation.

Size Control of Chiral Nanospheres Obtained via Nanoprecipitation of Helical Poly(phenylacetylene)s in the Absence of Surfactants.

Nanostructuration of dynamic helical polymers such as poly(phenylacetylene)s (PPAs) depends on the secondary structure adopted by the polymer and the functional group used to connect the chiral pendant to the PPA backbone. Thus, while PPAs with dynamic and flexible scaffolds (para- and meta-substituted, ω1<165°) generate by nanoprecipitation low polydisperse nanospheres with controllable size at different acetone/water mixtures, those with a quasi-static behavior and the presence of an extended, almost planar structure (ortho-substituted, ω1>165°), aggregate into a mixture of spherical and oval nanostructures whose size is not controlled. Photostability studies show that poly(phenylacetylene) particles are more stable to light irradiation than when dissolved macromolecularly. Moreover, the photostability of the particle depends on the secondary structure of the PPA and its screw sense excess. This fact, in combination with the encapsulation ability of these polymer particles, allows the creation of light stimuli-responsive nanocarriers, whose cargo can be delivered by light irradiation.

2,2'-Tethered Binaphthyl-Embedded One-Handed Helical Ladder Polymers: Impact of the Tether Length on Helical Geometry and Chiroptical Property.

Synthetic breakthroughs diversify the molecules and polymers available to chemists. We now report the first successful synthesis of a series of optically-pure 2,2'-tethered binaphthyl-embedded helical ladder polymers based on quantitative and chemoselective ladderization by the modified alkyne benzannulations using the 4-alkoxy-2,6-dimethylphenylethynyl group as the alkyne source, inaccessible by the conventional approach lacking the 2,6-dimethyl substituents. Due to the defect-free helix formation, the circular dichroism signal increased by more than 6 times the previously reported value. The resulting helical secondary structure can be fine-tuned by controlling the binaphthyl dihedral angle in the repeating unit with variations in the 2,2'-alkylenedioxy tethering groups by one carbon atom at a time. The optimization of the helical ladder structures led to a strong circularly polarized luminescence with a high fluorescence quantum yield (28 %) and luminescence dissymmetry factor (2.6×10-3 ).

Helix-Sense-Selective Memory Polymerization of Biphenylylacetylenes Bearing Carboxy and Amino Groups in Water.

We report the helix-sense-selective memory polymerization (HSMP) of achiral biphenylylacetylenes bearing carboxy and amino pendant groups in the presence of basic and acidic chiral guests in water, respectively. The HSMP proceeds in a highly helix-sense-selective manner driven by noncovalent chiral ionic interactions between the monomers and guests under kinetic control, producing the one-handed helical polymers with a static memory of helicity in one-pot during the polymerization in a very short time, accompanied by amplification of asymmetry. The carboxy-bound helicity-memorized polymer self-assembles into a cholesteric liquid crystal in concentrated water, in which a variety of basic achiral fluorophores further co-assembles to form supramolecular helical aggregates that exhibit an induced circularly polarized luminescence in a color tunable manner.

Compressible Hydrogels with Stabilized Chirality from Thermoresponsive Helical Dendronized Poly(phenylacetylene)s.

Fabrication of chiral hydrogels from thermoresponsive helical dendronized phenylacetylene copolymers (PPAs) carrying three-fold dendritic oligoethylene glycols (OEGs) is reported. Three different temperatures, i.e. below or above cloud point temperatures (Tcps) of the copolymers, and under freezing condition, were utilized, affording thermoresponsive hydrogels with different morphologies and mechanical properties. At room temperature, transparent hydrogels were obtained through crosslinking among different copolymer chains. Differently, opaque hydrogels with much improved mechanical properties were formed at elevated temperatures through crosslinking from the thermally dehydrated and collapsed copolymer aggregates, leading to heterogeneity for the hydrogels with highly porous morphology. While crosslinking at freezing temperature synergistically through ice templating, these amphiphilic dendronized copolymers formed hydrogels with highly porous lamellar structures, which exhibited remarkable compressible properties as human articular cartilage with excellent fatigue resistance. Amphiphilicity of the dendronized copolymers played a pivotal role in modulating the network formation during the gelation, as well as morphology and mechanical performance of the resulting hydrogels. Through crosslinking, these dendronized copolymers featured with typical dynamic helical conformations were transformed into hydrogels with unprecedently stabilized helicities due to the restrained chain mobilities in the three-dimensional networks.

One-Handed Covalent Helical Ladder Polymers: The Dawn of a Tailorable Class of Chiral Functional Materials.

In the last decades, chemists have developed methods to synthesize helical molecular architectures using a combination of covalent and non-covalent interactions. Very recently, the new class of completely covalent, one-handed helical ladder polymers has vigorously emerged. Such polymers can be rationally and programmably obtained through an approach guided by the principles of chirality-assisted-synthesis (CAS) and making use synergically of two disciplines that have so far rarely interacted: non-planar chiral π-conjugated synthons and ladder polymer chemistry. The precise programmability of the 3D structure and new mechanical and chiroptical properties will lead to potential applications in areas such as enantiorecognition, catalysis, spintronics and chiral-related optoelectronics. This minireview examines the emerging field of one-handed helical ladder polymers, analyzing their synthesis, applications, and limitations.

Synthesis and Conformational Behaviors of Unnatural Peptides Alternating Chiral and Achiral α,α-Disubstituted α-Amino Acid Units.

The development of peptidomimetics to modulate the conformational profile of peptides has been extensively studied in the fields of biological and medicinal chemistry. However, large-scale synthesis of peptidomimetics with both an ordered sequence and a controlled secondary structure is highly challenging. In this paper, the framework of peptidomimetics has been designed to be alternating an achiral α,α-disubstituted α-amino acid unit and a chiral α-methylphenylalanine unit. The polymers are synthesized via invented Ugi reaction-based polycondensation technique. The chiral higher-order structures of the alternating peptides are evaluated mainly through circular dichroism (CD) spectroscopy. The UV-Vis and CD spectra of the polymers in three solvents are systematically measured at various temperatures. The anisotropic factors of CD (gCD ) values are calculated to know the chiroptical response. The results indicate the characteristic conformational behaviors. In a polar solvent, the hydrogen bonds between the N-H group of MePhe unit and the C=O of α,α-diphenylglycine unit outweigh the intraresidue hydrogen bonds in α,α-diphenylglycine unit, leading to the formation of a prevailing preferred-handed 310 -helical conformation. On the other hand, in a less polar solvent, the intrachain hydrogen bonds switch to intraresidue hydrogen bonds in α,α-diphenylglycine unit, which make the polymer adopting a prevailing extended planar C5 -conformation.

Controlled Synthesis, Chiral Assembly, and Circularly Polarized Luminescence of Poly(Phenyl Isocyanide)-Block-Polyfluorene Copolymers.

In this work, π-conjugated block copolymers consisting of poly(phenyl isocyanide) (PPI) and polyfluorene (PF) segments are facilely prepared by one-pot sequential polymerization of phenyl isocyanide (monomer 1) and 7-bromo-9,9-dioctylfluorene-2-boronic acid pinacol ester (monomer 2). The Pd(II)-terminated PPI is first prepared via polymerizing monomer 1 catalyzed with phenyl alkyne-Pd(II) complex and then utilized to initiate the controlled Suzuki cross-coupling polymerization of monomer 2, yielding various PPI-b-PF copolymers possessing controlled molar mass and narrow dispersity. Owing to the helical conformation of PPI segment and π-conjugated structure of PF segment, PPI-b-PF copolymers present distinctive optical property and fascinating chiral self-assembly behavior. During the self-assembly process, chirality transfer from helical PPI block to the supramolecular aggregates of helical nanofibers occurs to afford optically active helical nanofibers with high optical activity. Furthermore, the self-assembled helical nanofibers exhibit excellent circularly polarized luminescence performance.

Diastereomeric multi-chiral pendant groups: Their key role in stimuli-responsive polymeric responses.

Chiral information transmission in helical polymers bearing multi-chiral pendant groups is usually determined by the absolute configuration of the first chiral center. The second chiral residue usually has low-to-null influence in the macromolecular handedness of the polymer, due to its remote position respect to the polyene main chain. Here, we demonstrate how the stimuli responsive properties of diastereomeric polymers, obtained by changing the absolute configuration of the second chiral center, are different due to the unlike properties of diastereoisomers.

One-Handed Helical Polyacetylenes Bearing Axially-Chiral 2-Arylpyridyl-N-Oxide Units for Efficient Chromatographic Enantioseparation of Chiral Aromatic and Aliphatic Alcohols.

A series of poly(biarylylacetylene)s (PBAs) bearing axially-chiral (S)-and (R)-pyridyl-N-oxide residues with a methoxy, propoxy, or acetyloxy substituent at the 3-position of the biaryl units was synthesized. All the PBAs formed a preferred-handed helix, while the helical sense preference was varied depending on the substituents despite the same twist-sense of the biaryl units. Among them, the propoxy-bound helical PBA showed an exceptionally high chiral recognition ability as a chiral stationary phase (CSP) for high-performance liquid chromatography (HPLC) and efficiently resolved not only various chiral aromatic alcohols, but also a variety of chiral aliphatic alcohols; the latter still remains difficult to resolve by commercially-available CSPs in HPLC. Such practically-useful both handed helical PBA-based CSPs can be produced from the racemic PBA composed of fully racemic monomer units through deracemization of the biaryl units with a chiral alcohol.

Remote Control of One-Handed Helicity in Polyacetylenes through Flexible Spacers in Water: Impact of the Spacer Length.

We report the unprecedented sergeants and soldiers (S&S)-type remote control of one-handed helicity in copolymers of chiral/achiral biphenylylacetylenes bearing amphiphilic oligo(ethylene glycol) (OEG) side chains. A small amount of chiral binaphthyl residues (≤10 mol %) introduced at the terminal of the achiral OEG spacers as many as 80 bonds away from the polymer backbones induced a complete one-handed helix in water through preferential intramolecular encapsulation of the binaphthyl groups within a cavity of the copolymers. A fully one-handed helix can be induced virtually independent of the OEG spacer length and concentrations. At a specific spacer length, however, its helix-sense was inverted. The copolymers also form an excess one-handed helix in organic solvents in an OEG spacer-length dependent manner, yet far from the polymer backbones. We show the superiority of the present covalent-bond driven S&S-type remote helicity control over the corresponding noncovalent helicity induction approach.

The Role of Polymer-AuNP Interaction in the Stimuli-Response Properties of PPA-AuNP Nanocomposites.

The helical sense control of dynamic helical polymers such as poly(phenylacetylene)s (PPAs) is greatly affected when they are conjugated to AuNPs through a strong thiol-Au connection, which restricts conformational changes at the polymer. Thus, the classical thiol-MNP bonds must be replaced by weaker ones, such as supramolecular amide-Au interactions. A straightforward preparation of the PPA-Au nanocomposite by reduction of a preformed PPA-Au3+ complex cannot be used due to a redox reaction between the two components of the complex which degrades the polymer. To avoid the interaction between the PPA and the Au3+ ions before the reduction takes place, the metal ions are added to the polymer solution capped as a TOAB complex, which keeps the PPA stable due to the lack of PPA-Au3+ interactions. Ulterior reduction of the Au3+ ions by NaBH4 affords the desired nanocomposite, where the AuNPs are stabilized by supramolecular anilide-AuNPs interactions. By using this approach, 3.7 nm gold nanoparticles are generated and aligned along the polymer chain with a regular distance between particles of 6 nm that corresponds to two helical pitches. These nanocomposites show stimuli-responsive properties and are also able to form macroscopically chiral nanospheres with tunable size.

Helix-Sense-Selective Polymerization of Achiral Monomers for the Preparation of Chiral Helical Polyacetylenes Showing Intense CPL in Solid Film State.

Polymer-based circularly polarized luminescent (CPL) materials have attracted ever-increasing interest. However, to construct CPL materials from achiral monomers is still a big challenge. Here, a series of chiral helical substituted polyacetylenes are prepared by helix-sense-selective polymerization (HSSP) of achiral acetylenic monomers (achiral monomer + fluorescent monomer). HSSPs are accomplished in a bi-solvent mixture consisting of chloroform and chiral α-pinene (chiral component). Chirality transfers from the chiral component to the helical copolymers during polymerization, thereby endowing the copolymers with helical chirality. The resulting copolymers are then fabricated into blend films which exhibit intense optical activity and CPL. The monomer ratio and the physical state of the copolymers have significant impacts on their chiroptical and CPL properties. The maximum luminescence dissymmetry factor of the blend films can be up to 1.3 × 10-2 . The universality of the established strategy for exploring polymer-based CPL materials is demonstrated by using different achiral fluorescent monomers. The present work opens a novel alternative for developing CPL-active polymeric materials starting from achiral monomers.