Cryo-EM Structure of a Relaxase Reveals the Molecular Basis of DNA Unwinding during Bacterial Conjugation.

Relaxases play essential roles in conjugation, the main process by which bacteria exchange genetic material, notably antibiotic resistance genes. They are bifunctional enzymes containing a trans-esterase activity, which is responsible for nicking the DNA strand to be transferred and for covalent attachment to the resulting 5'-phosphate end, and a helicase activity, which is responsible for unwinding the DNA while it is being transported to a recipient cell. Here we show that these two activities are carried out by two conformers that can both load simultaneously on the origin of transfer DNA. We solve the structure of one of these conformers by cryo electron microscopy to near-atomic resolution, elucidating the molecular basis of helicase function by relaxases and revealing insights into the mechanistic events taking place in the cell prior to substrate transport during conjugation.

Understanding the effects of targeted modifications on the 1 : 2 Choline And GEranate structure.

1 : 2 Choline-and-geranate (CAGE) is an ionic liquid (IL) widely studied for its biomedical applications. However, both its industrial-scale preparation and its long-term storage are problematic so finding more suitable candidates which retain its advantageous properties is crucial. As a first step towards this we have conducted a targeted modification study to understand the effects of specific functional groups on the properties of CAGE. 1 : 2 Choline-and-octanoate and 1 : 2 butyltrimethylammonium-and-octanoate were synthesised and their thermal and rheological properties examined in comparison to those of CAGE. Using differential scanning calorimetry and polarising microscopy, the model compound was found to be an isotropic liquid, while the analogues were room-temperature liquid-crystals which transition to isotropic liquids upon heating. Dynamic mechanical analysis showed that the thermal behaviour of the studied systems was even more complex, with the ILs also undergoing a thermally-activated relaxation process. Furthermore, we have used electron paramagnetic resonance (EPR) spectroscopy, along with a variety of spin probes with different functional groups, in order to understand the chemical environment experienced by solutes in each system. The EPR spectra indicate that the radicals experience two distinct environments (polar and nonpolar) in the liquid-crystalline phase, but only one average environment in the isotropic phase. The liquid-crystalline phase experiments also showed that the relative populations of the two domains depend on the nature of the solutes, with polar or strongly hydrogen-bonding solutes preferring the polar domain. For charged solutes, the EPR spectra showed line-broadening, suggesting that their ionic nature leads to complex, unresolved interactions.

Continuous-wave room-temperature diamond maser.

The maser-the microwave progenitor of the optical laser-has been confined to relative obscurity owing to its reliance on cryogenic refrigeration and high-vacuum systems. Despite this, it has found application in deep-space communications and radio astronomy owing to its unparalleled performance as a low-noise amplifier and oscillator. The recent demonstration of a room-temperature solid-state maser that utilizes polarized electron populations within the triplet states of photo-excited pentacene molecules in a p-terphenyl host paves the way for a new class of maser. However, p-terphenyl has poor thermal and mechanical properties, and the decay rates of the triplet sublevel of pentacene mean that only pulsed maser operation has been observed in this system. Alternative materials are therefore required to achieve continuous emission: inorganic materials that contain spin defects, such as diamond and silicon carbide, have been proposed. Here we report a continuous-wave room-temperature maser oscillator using optically pumped nitrogen-vacancy defect centres in diamond. This demonstration highlights the potential of room-temperature solid-state masers for use in a new generation of microwave devices that could find application in medicine, security, sensing and quantum technologies.

Black Titania and Niobia within Ten Minutes - Mechanochemical Reduction of Metal Oxides with Alkali Metal Hydrides.

Partially or fully reduced transition metal oxides show extraordinary electronic and catalytic properties but are usually prepared by high temperature reduction reactions. This study reports the systematic investigation of the fast mechanochemical reduction of rutile-type TiO2 and H-Nb2 O5 to their partially reduced black counterparts applying NaH and LiH as reducing agents. Milling time and oxide to reducing agent ratio show a large influence on the final amount of reduced metal ions in the materials. For both oxides LiH shows a higher reducing potential than NaH. An intercalation of Li+ into the structure of the oxides was proven by PXRD and subsequent Rietveld refinements as well as 6 Li solid-state NMR spectroscopy. The products showed a decreased band gap and the presence of unpaired electrons as observed by EPR spectroscopy, proving the successful reduction of Ti4+ and Nb5+ . Furthermore, the developed material exhibits a significantly enhanced photocatalytic performance towards the degradation of methylene blue compared to the pristine oxides. The presented method is a general, time efficient and simple method to obtain reduced transition metal oxides.

Anion and ether group influence in protic guanidinium ionic liquids.

Ionic liquids are attractive liquid materials for many advanced applications. For targeted design, in-depth knowledge about their structure-property-relations is urgently needed. We prepared a set of novel protic ionic liquids (PILs) with a guanidinium cation with either an ether or alkyl side chain and different anions. While being a promising cation class, the available data is insufficient to guide design. We measured thermal and transport properties, nuclear magnetic resonance (NMR) spectra as well as liquid and crystalline structures supported by ab initio computations and were able to obtain a detailed insight into the influence of the anion and the ether substitution on the physical and spectroscopic properties. For the PILs, hydrogen bonding is the main interaction between cation and anion and the H-bond strength is inversely related to the proton affinity of the constituting acid and correlated to the increase of 1H and 15N chemical shifts. Using anions from acids with lower proton affinity leads to proton localization on the cation as evident from NMR spectra and self-diffusion coefficients. In contrast, proton exchange was evident in ionic liquids with triflate and trifluoroacetate anions. Using imide-type anions and ether side groups decreases glass transitions as well as fragility, and accelerated dynamics significantly. In case of the ether guanidinium ionic liquids, the conformation of the side chain adopts a curled structure as the result of dispersion interactions, while the alkyl chains prefer a linear arrangement.

Evidence of AlII Radical Addition to Benzene.

Electrophilic AlIII species have long dominated the aluminum reactivity towards arenes. Recently, nucleophilic low-valent AlI aluminyl anions have showcased oxidative additions towards arenes C-C and/or C-H bonds. Herein, we communicate compelling evidence of an AlII radical addition reaction to the benzene ring. The electron reduction of a ligand stabilized precursor with KC8 in benzene furnishes a double addition to the benzene ring instead of a C-H bond activation, producing the corresponding cyclohexa-1,3(orl,4)-dienes as Birch-type reduction product. X-ray crystallographic analysis, EPR spectroscopy, and DFT results suggest this reactivity proceeds through a stable AlII radical intermediate, whose stability is a consequence of a rigid scaffold in combination with strong steric protection.

Palladium Terminal Imido Complexes with Nitrene Character.

Whereas triplet-nitrene complexes of the late transition metals are isolable and key intermediates in catalysis, singlet-nitrene ligands remain elusive. Herein we communicate three such palladium terminal imido complexes with singlet ground states. UV-vis-NIR electronic spectroscopy with broad bands up to 1400 nm as well as high-level computations (DFT, STEOM-CCSD, CASSCF/NEVPT2, EOS analysis) and reactivity studies suggest significant palladium(0) singlet-nitrene character. Although the aliphatic nitrene complexes proved to be too reactive for isolation in analytically pure form as a result of elimination of isobutylene, the aryl congener could be characterized by SC-XRD, elemental analysis, IR-, NMR spectroscopy, and HRMS. The complexes' distinguished ambiphilicity allows them to activate hexafluorobenzene, triphenylphosphine, and pinacol borane, catalytically dehydrogenate cyclohexene, and aminate ethylene via nitrene transfer at or below room temperature.

Effect of the cation structure on the properties of homobaric imidazolium ionic liquids.

In this work we investigate the structure-property relationships in a series of alkylimidazolium ionic liquids with almost identical molecular weight. Using a combination of theoretical calculations and experimental measurements, we have shown that re-arranging the alkyl side chain or adding functional groups results in quite distinct features in the resultant ILs. The synthesised ILs, although structurally very similar, cover a wide spectrum of properties ranging from highly fluid, glass forming liquids to high melting point crystalline salts. Theoretical ab initio calculations provide insight on minimum energy orientations for the cations, which then are compared to experimental X-ray crystallography measurements to extract information on hydrogen bonding and to verify our understanding of the studied structures. Molecular dynamics simulations of the simplest (core) ionic liquids are used in order to help us interpret our experimental results and understand better why methylation of C2 position of the imidazolium ring results in ILs with such different properties compared to their non-methylated analogues.

Novel Phosphonium-Based Ionic Liquid Electrolytes for Battery Applications.

In this study, we address the fundamental question of the physicochemical and electrochemical properties of phosphonium-based ionic liquids containing the counter-ions bis(trifluoromethanesulfonyl)imide ([TFSI]-) and bis(fluorosulfonyl)imide ([FSI]-). To clarify these structure-property as well as structure-activity relationships, trimethyl-based alkyl- and ether-containing phosphonium ILs were systematically synthesized, and their properties, namely density, flow characteristics, alkali metal compatibility, oxidative stability, aluminum corrosivity as well as their use in Li-ion cells were examined comprehensively. The variable moiety on the phosphonium cation exhibited a chain length of four and five, respectively. The properties were discussed as a function of the side chain, counter-ion and salt addition ([Li][TFSI] or [Li][FSI]). High stability coupled with good flow characteristics were found for the phosphonium IL [P1114][TFSI] and the mixture [P1114][TFSI] + [Li][TFSI], respectively.

Curled cation structures accelerate the dynamics of ionic liquids.

Ionic liquids are modern liquid materials with potential and actual implementation in many advanced technologies. They combine many favourable and modifiable properties but have a major inherent drawback compared to molecular liquids - slower dynamics. In previous studies we found that the dynamics of ionic liquids are significantly accelerated by the introduction of multiple ether side chains into the cations. However, the origin of the improved transport properties, whether as a result of the altered cation conformation or due to the absence of nanostructuring within the liquid as a result of the higher polarity of the ether chains, remained to be clarified. Therefore, we prepared two novel sets of methylammonium based ionic liquids; one set with three ether substituents and another set with three butyl side chains, in order to compare their dynamic properties and liquid structures. Using a range of anions, we show that the dynamics of the ether-substituted cations are systematically and distinctly accelerated. Liquefaction temperatures are lowered and fragilities increased, while at the same time cation-anion distances are slightly larger for the alkylated samples. Furthermore, pronounced liquid nanostructures were not observed. Molecular dynamics simulations demonstrate that the origin of the altered properties of the ether substituted ionic liquids is primarily due to a curled ether chain conformation, in contrast to the alkylated cations where the alkyl chains retain a linear conformation. Thus, the observed structure-property relations can be explained by changes in the geometric shape of the cations, rather than by the absence of a liquid nanostructure. Application of quantum chemical calculations to a simplified model system revealed that intramolecular hydrogen-bonding is responsible for approximately half of the stabilisation of the curled ether-cations, whereas the other half stems from non-specific long-range interactions. These findings give more detailed insights into the structure-property relations of ionic liquids and will guide the development of ionic liquids that do not suffer from slow dynamics.

Ether functionalisation, ion conformation and the optimisation of macroscopic properties in ionic liquids.

Ionic liquids are an attractive material class due to their wide liquid range, intrinsic ionic conductivity, and high chemical as well as electrochemical stability. However, the widespread use of ionic liquids is hindered by significantly higher viscosities compared to conventional molecular solvents. In this work, we show how the transport properties of ionic liquids can be altered significantly, even for isostructural ions that have the same backbone. To this end, structure-property relationships have been determined for a set of 16 systematically varied representative ionic liquids. Variations in molecular structure include ammonium vs. phosphonium, ether vs. alkyl side chains, and rigid vs. flexible anions. Ab initio calculations are used to relate molecular structures to the thermal, structural and transport properties of the ionic liquids. We find that the differences in properties of ether and alkyl functionalised ionic liquids are primarily dependent on minimum energy geometries, with the conformational flexibility of ether side chains appearing to be of secondary importance. We also show unprecedented correlations between anion conformational flexibility and transport properties. Critically, increasing fluidity upon consecutive introduction of ether side chains and phosphonium centres into the cation is found to be dependent on whether the anion is flexible or rigid. We demonstrate that targeted design of functional groups based on structure-property relationships can yield ionic liquids of exceptionally high fluidity.

Equilibrium Formation of Stable All-Silicon Versions of 1,3-Cyclobutanediyl.

Main group analogues of cyclobutane-1,3-diyls are fascinating due to their unique reactivity and electronic properties. So far only heteronuclear examples have been isolated. Here we report the isolation and characterization of all-silicon 1,3-cyclobutanediyls as stable closed-shell singlet species from the reversible reactions of cyclotrisilene c-Si3 Tip4 (Tip=2,4,6-triisopropylphenyl) with the N-heterocyclic silylenes c-[(CR2 CH2 )(NtBu)2 ]Si: (R=H or methyl) with saturated backbones. At elevated temperatures, tetrasilacyclobutenes are obtained from these equilibrium mixtures. The corresponding reaction with the unsaturated N-heterocyclic silylene c-(CH)2 (NtBu)2 Si: proceeds directly to the corresponding tetrasilacyclobutene without detection of the assumed 1,3-cyclobutanediyl intermediate.

Exploiting Excited-State Aromaticity To Design Highly Stable Singlet Fission Materials.

Singlet fission, the process of forming two triplet excitons from one singlet exciton, is a characteristic reserved for only a handful of organic molecules due to the atypical energetic requirement for low energy excited triplet states. The predominant strategy for achieving such a trait is by increasing ground state diradical character; however, this greatly reduces ambient stability. Herein, we exploit Baird's rule of excited state aromaticity to manipulate the singlet-triplet energy gap and create novel singlet fission candidates. We achieve this through the inclusion of a [4n] 5-membered heterocycle, whose electronic resonance promotes aromaticity in the triplet state, stabilizing its energy relative to the singlet excited state. Using this theory, we design a family of derivatives of indolonaphthyridine thiophene (INDT) with highly tunable excited state energies. Not only do we access novel singlet fission materials, they also exhibit excellent ambient stability, imparted due to the delocalized nature of the triplet excited state. Spin-coated films retained up to 85% activity after several weeks of exposure to oxygen and light, while analogous films of TIPS-pentacene showed full degradation after 4 days, showcasing the excellent stability of this class of singlet fission scaffold. Extension of our theoretical analysis to almost ten thousand candidates reveals an unprecedented degree of tunability and several thousand potential fission-capable candidates, while clearly demonstrating the relationship between triplet aromaticity and singlet-triplet energy gap, confirming this novel strategy for manipulating the exchange energy in organic materials.

Potential for spin-based information processing in a thin-film molecular semiconductor.

Organic semiconductors are studied intensively for applications in electronics and optics, and even spin-based information technology, or spintronics. Fundamental quantities in spintronics are the population relaxation time (T1) and the phase memory time (T2): T1 measures the lifetime of a classical bit, in this case embodied by a spin oriented either parallel or antiparallel to an external magnetic field, and T2 measures the corresponding lifetime of a quantum bit, encoded in the phase of the quantum state. Here we establish that these times are surprisingly long for a common, low-cost and chemically modifiable organic semiconductor, the blue pigment copper phthalocyanine, in easily processed thin-film form of the type used for device fabrication. At 5 K, a temperature reachable using inexpensive closed-cycle refrigerators, T1 and T2 are respectively 59 ms and 2.6 µs, and at 80 K, which is just above the boiling point of liquid nitrogen, they are respectively 10 µs and 1 µs, demonstrating that the performance of thin-film copper phthalocyanine is superior to that of single-molecule magnets over the same temperature range. T2 is more than two orders of magnitude greater than the duration of the spin manipulation pulses, which suggests that copper phthalocyanine holds promise for quantum information processing, and the long T1 indicates possibilities for medium-term storage of classical bits in all-organic devices on plastic substrates.

Crystal structure of the FimD usher bound to its cognate FimC-FimH substrate.

Type 1 pili are the archetypal representative of a widespread class of adhesive multisubunit fibres in Gram-negative bacteria. During pilus assembly, subunits dock as chaperone-bound complexes to an usher, which catalyses their polymerization and mediates pilus translocation across the outer membrane. Here we report the crystal structure of the full-length FimD usher bound to the FimC-FimH chaperone-adhesin complex and that of the unbound form of the FimD translocation domain. The FimD-FimC-FimH structure shows FimH inserted inside the FimD 24-stranded ß-barrel translocation channel. FimC-FimH is held in place through interactions with the two carboxy-terminal periplasmic domains of FimD, a binding mode confirmed in solution by electron paramagnetic resonance spectroscopy. To accommodate FimH, the usher plug domain is displaced from the barrel lumen to the periplasm, concomitant with a marked conformational change in the ß-barrel. The amino-terminal domain of FimD is observed in an ideal position to catalyse incorporation of a newly recruited chaperone-subunit complex. The FimD-FimC-FimH structure provides unique insights into the pilus subunit incorporation cycle, and captures the first view of a protein transporter in the act of secreting its cognate substrate.

An antibody that prevents serpin polymerisation acts by inducing a novel allosteric behaviour.

Serpins are important regulators of proteolytic pathways with an antiprotease activity that involves a conformational transition from a metastable to a hyperstable state. Certain mutations permit the transition to occur in the absence of a protease; when associated with an intermolecular interaction, this yields linear polymers of hyperstable serpin molecules, which accumulate at the site of synthesis. This is the basis of many pathologies termed the serpinopathies. We have previously identified a monoclonal antibody (mAb4B12) that, in single-chain form, blocks α1-antitrypsin (α1-AT) polymerisation in cells. Here, we describe the structural basis for this activity. The mAb4B12 epitope was found to encompass residues Glu32, Glu39 and His43 on helix A and Leu306 on helix I. This is not a region typically associated with the serpin mechanism of conformational change, and correspondingly the epitope was present in all tested structural forms of the protein. Antibody binding rendered ß-sheet A - on the opposite face of the molecule - more liable to adopt an 'open' state, mediated by changes distal to the breach region and proximal to helix F. The allosteric propagation of induced changes through the molecule was evidenced by an increased rate of peptide incorporation and destabilisation of a preformed serpin-enzyme complex following mAb4B12 binding. These data suggest that prematurely shifting the ß-sheet A equilibrium towards the 'open' state out of sequence with other changes suppresses polymer formation. This work identifies a region potentially exploitable for a rational design of ligands that is able to dynamically influence α1-AT polymerisation.

Probing the Solution Structure of IκB Kinase (IKK) Subunit γ and Its Interaction with Kaposi Sarcoma-associated Herpes Virus Flice-interacting Protein and IKK Subunit ß by EPR Spectroscopy.

Viral flice-interacting protein (vFLIP), encoded by the oncogenic Kaposi sarcoma-associated herpes virus (KSHV), constitutively activates the canonical nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) pathway. This is achieved through subversion of the IκB kinase (IKK) complex (or signalosome), which involves a physical interaction between vFLIP and the modulatory subunit IKKγ. Although this interaction has been examined both in vivo and in vitro, the mechanism by which vFLIP activates the kinase remains to be determined. Because IKKγ functions as a scaffold, recruiting both vFLIP and the IKKα/ß subunits, it has been proposed that binding of vFLIP could trigger a structural rearrangement in IKKγ conducive to activation. To investigate this hypothesis we engineered a series of mutants along the length of the IKKγ molecule that could be individually modified with nitroxide spin labels. Subsequent distance measurements using electron paramagnetic resonance spectroscopy combined with molecular modeling and molecular dynamics simulations revealed that IKKγ is a parallel coiled-coil whose response to binding of vFLIP or IKKß is localized twisting/stiffening and not large-scale rearrangements. The coiled-coil comprises N- and C-terminal regions with distinct registers accommodated by a twist: this structural motif is exploited by vFLIP, allowing it to bind and subsequently activate the NF-κB pathway. In vivo assays confirm that NF-κB activation by vFLIP only requires the N-terminal region up to the transition between the registers, which is located directly C-terminal of the vFLIP binding site.

Comparative study of singlet oxygen production by photosensitiser dyes encapsulated in silicone: towards rational design of anti-microbial surfaces.

Surfaces with built-in antimicrobial activity have the potential to reduce hospital-acquired infections. One promising strategy is to create functionalised surfaces which, following illumination with visible light, are able to generate singlet oxygen under aerobic conditions. In contrast to antibiotics, the mechanism of bacterial kill by species derived from reactions with singlet oxygen is completely unselective, therefore offering little room for evolutionary adaptation. Here we consider five commercially available organic photosensitiser dyes encapsulated in silicone polymer that show varied antimicrobial activity. We correlate density functional theory calculations with UV-Vis spectroscopy, electron paramagnetic resonance spectroscopy and singlet oxygen production measurements in order to define and test the elements required for efficacious antimicrobial activity. Our approach forms the basis for the rational in silico design and spectroscopic screening of simple and efficient self-sterilising surfaces made from cheap, low toxicity photosensitiser dyes encapsulated in silicone.

Comparisons of subunit 5A and 5B isoenzymes of yeast cytochrome c oxidase.

Subunit 5 of Saccharomyces cerevisiae cytochrome c oxidase (CcO) is essential for assembly and has two isoforms, 5A and 5B. 5A is expressed under normoxic conditions, whereas 5B is expressed at very low oxygen tensions. As a consequence, COX5A-deleted strains (Δcox5A) have no or only low levels of CcO under normoxic conditions rendering them respiratory deficient. Previous studies have reported that respiratory growth could be restored by combining Δcox5A with mutations of ROX1 that encodes a repressor of COX5B expression. In these mutants, 5B isoenzyme expression level was 30-50% of wild-type (5A isoenzyme) and exhibited a maximum catalytic activity up to 3-fold faster than that of 5A isoenzyme. To investigate the origin of this effect, we constructed a mutant strain in which COX5B replaced COX5A downstream of the COX5A promoter. This strain expressed wild-type levels of the 5B isoenzyme, without the complication of additional effects caused by mutation of ROX1. When produced this way, the isoenzymes displayed no significant differences in their maximum catalytic activities or in their affinities for oxygen or cytochrome c. Hence the elevated activity of the 5B isoenzyme in the rox1 mutant is not caused simply by exchange of isoforms and must arise from an additional effect that remains to be resolved.

Exploiting the Symmetry of the Resonator Mode to Enhance PELDOR Sensitivity.

Pulsed electron paramagnetic resonance (EPR) spectroscopy using microwaves at two frequencies can be employed to measure distances between pairs of paramagnets separated by up to 10 nm. The method, combined with site-directed mutagenesis, has become increasingly popular in structural biology for both its selectivity and capability of providing information not accessible through more standard methods such as nuclear magnetic resonance and X-ray crystallography. Despite these advantages, EPR distance measurements suffer from poor sensitivity. One contributing factor is technical: since 65 MHz typically separates the pump and detection frequencies, they cannot both be located at the center of the pseudo-Lorentzian microwave resonance of a single-mode resonator. To maximize the inversion efficiency, the pump pulse is usually placed at the center of the resonance, while the observer frequency is placed in the wing, with consequent reduction in sensitivity. Here, we consider an alternative configuration: by spacing pump and observer frequencies symmetrically with respect to the microwave resonance and by increasing the quality factor, valuable improvement in the signal-to-noise ratio can be obtained.