Machine Learning Deciphered Molecular Mechanistics with Accurate Kinetic and Thermodynamic Prediction.

Time-lagged independent component analysis (tICA) and the Markov state model (MSM) have been extensively employed for extracting conformational dynamics and kinetic community networks from unbiased trajectory ensembles. However, these techniques may not be the optimal choice for elucidating transition mechanisms within low-dimensional representations, especially for intricate biosystems. Unraveling the association mechanism in such complex systems always necessitates permutations of several essential independent components or collective variables, a process that is inherently obscure and may require empirical knowledge for selection. To address these challenges, we have implemented an integrated unsupervised dimension reduction model: uniform manifold approximation and projection (UMAP) with hierarchy density-based spatial clustering of applications with noise (HDBSCAN). This approach effectively generates low-dimensional configurational embeddings. The hierarchical application of this architecture, in conjunction with MSM, reveals global kinetic connectivity while identifying local conformational states. Consequently, our methodology establishes a multiscale mechanistic elucidation framework. Leveraging the benefits of the uniform sample distribution and a denoising approach, our model demonstrates robustness in preserving global and local data structures compared to traditional dimension reduction methods in the field of MD analysis area. The interpretability of hyperparameter selection and compatibility with downstream tasks are cross-validated across various simulation data sets, utilizing both computational evaluation metrics and experimental kinetic observables. Furthermore, the predicted Mcl1-BH3 association kinetics (0.76 s-1) is in close agreement with surface plasmon resonance experiments (0.12 s-1), affirming the plausibility of the identified pathway composed of representative conformations. We anticipate that the devised workflow will serve as a foundational framework for studying recognition patterns in complex biological systems. Its contributions extend to the exploration of protein functional dynamics and rational drug design, offering a potent avenue for advancing research in these domains.

A global meta-analysis of yield-scaled N2 O emissions and its mitigation efforts for maize, wheat, and rice.

Maintaining or even increasing crop yields while reducing nitrous oxide (N2 O) emissions is necessary to reconcile food security and climate change, while the metric of yield-scaled N2 O emission (i.e., N2 O emissions per unit of crop yield) is at present poorly understood. Here we conducted a global meta-analysis with more than 6000 observations to explore the variation patterns and controlling factors of yield-scaled N2 O emissions for maize, wheat and rice and associated potential mitigation options. Our results showed that the average yield-scaled N2 O emissions across all available data followed the order wheat (322 g N Mg-1 , with the 95% confidence interval [CI]: 301-346) > maize (211 g N Mg-1 , CI: 198-225) > rice (153 g N Mg-1 , CI: 144-163). Yield-scaled N2 O emissions for individual crops were generally higher in tropical or subtropical zones than in temperate zones, and also showed a trend towards lower intensities from low to high latitudes. This global variation was better explained by climatic and edaphic factors than by N fertilizer management, while their combined effect predicted more than 70% of the variance. Furthermore, our analysis showed a significant decrease in yield-scaled N2 O emissions with increasing N use efficiency or in N2 O emissions for production systems with cereal yields >10 Mg ha-1 (maize), 6.6 Mg ha-1 (wheat) or 6.8 Mg ha-1 (rice), respectively. This highlights that N use efficiency indicators can be used as valuable proxies for reconciling trade-offs between crop production and N2 O mitigation. For all three major staple crops, reducing N fertilization by up to 30%, optimizing the timing and placement of fertilizer application or using enhanced-efficiency N fertilizers significantly reduced yield-scaled N2 O emissions at similar or even higher cereal yields. Our data-driven assessment provides some key guidance for developing effective and targeted mitigation and adaptation strategies for the sustainable intensification of cereal production.

Evidence for ground state coherence in a two-dimensional Kondo lattice.

Kondo lattices are ideal testbeds for the exploration of heavy-fermion quantum phases of matter. While our understanding of Kondo lattices has traditionally relied on complex bulk f-electron systems, transition metal dichalcogenide heterobilayers have recently emerged as simple, accessible and tunable 2D Kondo lattice platforms where, however, their ground state remains to be established. Here we present evidence of a coherent ground state in the 1T/1H-TaSe2 heterobilayer by means of scanning tunneling microscopy/spectroscopy at 340 mK. Our measurements reveal the existence of two symmetric electronic resonances around the Fermi energy, a hallmark of coherence in the spin lattice. Spectroscopic imaging locates both resonances at the central Ta atom of the charge density wave of the 1T phase, where the localized magnetic moment is held. Furthermore, the evolution of the electronic structure with the magnetic field reveals a non-linear increase of the energy separation between the electronic resonances. Aided by ab initio and auxiliary-fermion mean-field calculations, we demonstrate that this behavior is inconsistent with a fully screened Kondo lattice, and suggests a ground state with magnetic order mediated by conduction electrons. The manifestation of magnetic coherence in TMD-based 2D Kondo lattices enables the exploration of magnetic quantum criticality, Kondo breakdown transitions and unconventional superconductivity in the strict two-dimensional limit.

Aperiodic Modulation of Graphene Driven by Oxygen-Induced Reconstruction of Rh(110).

Artificial nanostructuring of graphene has served as a platform to induce variations in its structural and electronic properties, fostering the experimental observation of a wide and fascinating phenomenology. Here, we present an approach to graphene tuning, based on Rh(110) surface reconstruction induced by oxygen atoms intercalation. The resulting nanostructured graphene has been characterized by scanning tunneling microscopy (STM) complemented by low-energy electron microscopy (LEEM), micro low-energy electron diffraction (µ-LEED), micro angle-resolved photoemission spectroscopy (µ-ARPES), and micro X-ray photoelectron spectroscopy (µ-XPS) measurements under ultrahigh vacuum (UHV) conditions at room temperature (RT). It is found that by fine-tuning the O2 exposure amount, a mixture of missing row surface reconstructions of the metal surface below the graphene layer can be induced. This atomic rearrangement under the graphene layer results in aperiodic patterning of the two-dimensional (2D) material. The electronic structure of the resulting nanostructured graphene is dominated by a linear dispersion of the Dirac quasiparticles, characteristic of its free-standing state but with a p-doping character. The local effects of the underlying missing rows on the interfacial chemistry and on the quasiparticle scattering processes in graphene are studied using atomically resolved STM images. The possibilities offered by this nanostructuring approach, which consists in inducing surface reconstructions under graphene, could provide a novel tuning strategy for this 2D material.

Enhanced Light Extraction Efficiency by Self-Masking Technology with Carbonized Photoresist for Light-Emitting Diodes.

This work investigates a self-masking technology for roughening the surface of light-emitting diodes (LEDs). The carbonized photoresist with a naturally nano/micro-textured rough surface was used as a mask layer. After growing the Si3N4 passivation layer on LEDs, the texture pattern of the mask layer was transferred to the surface of the passivation layer via reactive ion beam (RIE) dry etching, resulting in LEDs with nano-textured surfaces. This nano-textured surface achieved by self-masking technology can alleviate the total internal reflection at the top interface and enhance light scattering, thereby improving the light extraction efficiency. As a result, the wall-plug efficiency (WPE) and external quantum efficiency (EQE) of rough-surface LEDs reached 53.9% and 58.8% at 60 mA, respectively, which were improved by 10.3% and 10.5% compared to that of the flat-surface Si3N4-passivated LED. Additionally, at the same peak, both LEDs emit a wavelength of 451 nm at 350 mA. There is also almost no difference between the I-V characteristics of LEDs before and after roughening. The proposed self-masking surface roughening technology provides a strategy for LEE enhancement that is both cost-effective and compatible with conventional fabrication processes.

One-step laser synthesis platinum nanostructured 3D porous graphene: A flexible dual-functional electrochemical biosensor for glucose and pH detection in human perspiration.

There has been a recent increase in the demand for wearable sensors for sweat glucose monitoring to facilitate diabetes management in a patient-friendly and non-invasive manner. To address this issue, the key challenge lies in the design of flexible sensors with high conductivity, miniaturized patterning, and environmental friendliness. Herein, we introduce a flexible electrochemical sensing system for glucose and pH detection based on one-step laser-scribed PtNPs nanostructured 3D porous laser-scribed graphene (LSG). The as-prepared nanocomposites can synchronously possess hierarchical porous graphene architectures, whereas PtNPs can significantly enhance their sensitivity and electrocatalytic activity. Benefiting from these advantages, the fabricated Pt-HEC/LSG biosensor exhibited a high sensitivity of 69.64 µA mM-1 cm-2 as well as a low limit of detection (LOD) of 0.23 µM at a detection range of 5-3000 µM (covering the glucose range in sweat). Moreover, the pH sensor was functionalized with polyaniline (PANI) on a Pt-HEC/LSG electrode, and it also exhibited high sensitivity (72.4 mV/pH) in the linear range of pH 4-8. The feasibility of the biosensor was confirmed by analyzing human perspiration during physical exercise. This dual-functional electrochemical biosensor displayed excellent performance, including a low detection limit, high selectivity, and great flexibility. These results confirm that the proposed dual-functional flexible electrode and fabrication process are highly promising for application in human sweat-based electrochemical glucose and pH sensors.

Growth of 1D ClAlPc molecular chains mediated by graphene moiré patterns.

The on-surface formation of iso-oriented 1D molecular architectures, with high structural perfection, on 2D materials has been a long-sought objective. However, such realization has been troublesome and limited, and it still remains an experimental challenge. Here, the quasi-1D stripe-like moiré pattern, arising at the interface of graphene grown on Rh(110), has been used to guide the formation of 1D molecular wires of π-conjugated, non-planar, chloro-aluminum phthalocyanine (ClAlPc) molecules, brought together by van der Waals interactions. Using scanning tunnelling microscopy (STM) under ultra-high vacuum (UHV) at 40 K, the preferential adsorption orientations of the molecules at low coverages have been investigated. The results shed light on the potential signature of graphene lattice symmetry breaking, induced by the incommensurate quasi-1D moiré pattern of Gr/Rh(110), as the subtle mechanism behind this templated growth of 1D molecular structures. For coverages close to 1 ML, the molecule-molecule interactions favor a closely packed square lattice arrangement. The present work provides new insights to tailor 1D molecular structures on graphene grown on a non-hexagonal metal substrate.

Lateral Heterostructures of Graphene and h-BN with Atomic Lattice Coherence and Tunable Rotational Order.

In-plane heterostructures of graphene and hexagonal boron nitride (h-BN) exhibit exceptional properties, which are highly sensitive to the structure of the alternating domains. Nevertheless, achieving accurate control over their structural properties, while keeping a high perfection at the graphene-h-BN boundaries, still remains a challenge. Here, the growth of lateral heterostructures of graphene and h-BN on Rh(110) surfaces is reported. The choice of the 2D material, grown firstly, determines the structural properties of the whole heterostructure layer, allowing to have control over the rotational order of the domains. The atomic-scale observation of the boundaries demonstrates a perfect lateral matching. In-plane heterostructures floating over an oxygen layer have been successfully obtained, enabling to observe intervalley scattering processes in graphene regions. The high tuning capabilities of these heterostructures, along with their good structural quality, even around the boundaries, suggest their usage as test beds for fundamental studies aiming at the development of novel nanomaterials with tailored properties.

Observation of Superconducting Collective Modes from Competing Pairing Instabilities in Single-Layer NbSe2.

In certain unconventional superconductors with sizable electronic correlations, the availability of closely competing pairing channels leads to characteristic soft collective fluctuations of the order parameters, which leave fingerprints in many observables and allow the phase competition to be scrutinized. Superconducting layered materials, where electron-electron interactions are enhanced with decreasing thickness, are promising candidates to display these correlation effects. In this work, the existence of a soft collective mode in single-layer NbSe2 , observed as a characteristic resonance excitation in high-resolution tunneling spectra is reported. This resonance is observed along with higher harmonics, its frequency Ω/2Δ is anticorrelated with the local superconducting gap Δ, and its amplitude gradually vanishes by increasing the temperature and upon applying a magnetic field up to the critical values (TC and HC2 ), which sets an unambiguous link to the superconducting state. Aided by a microscopic model that captures the main experimental observations, this resonance is interpreted as a collective Leggett mode that represents the fluctuation toward a proximate f-wave triplet state, due to subleading attraction in the triplet channel. These findings demonstrate the fundamental role of correlations in superconducting 2D transition metal dichalcogenides, opening a path toward unconventional superconductivity in simple, scalable, and transferable 2D superconductors.

Proximity Effects on the Charge Density Wave Order and Superconductivity in Single-Layer NbSe2.

Collective electronic states such as the charge density wave (CDW) order and superconductivity (SC) respond sensitively to external perturbations. Such sensitivity is dramatically enhanced in two dimensions (2D), where 2D materials hosting such electronic states are largely exposed to the environment. In this regard, the ineludible presence of supporting substrates triggers various proximity effects on 2D materials that may ultimately compromise the stability and properties of the electronic ground state. In this work, we investigate the impact of proximity effects on the CDW and superconducting states in single-layer (SL) NbSe2 on four substrates of diverse nature, namely, bilayer graphene (BLG), SL-boron nitride (h-BN), Au(111), and bulk WSe2. By combining low-temperature (340 mK) scanning tunneling microscopy/spectroscopy and angle-resolved photoemission spectroscopy, we compare the electronic structure of this prototypical 2D superconductor on each substrate. We find that, even when the electronic band structure of SL-NbSe2 remains largely unaffected by the substrate except when placed on Au(111), where a charge transfer occurs, both the CDW and SC show disparate behaviors. On the insulating h-BN/Ir(111) substrate and the metallic BLG/SiC(0001) substrate, both the 3 × 3 CDW and superconducting phases persist in SL-NbSe2 with very similar properties, which reveals the negligible impact of graphene on these electronic phases. In contrast, these collective electronic phases are severely weakened and even absent on the bulk insulating WSe2 substrate and the metallic single-crystal Au(111) substrate. Our results provide valuable insights into the fragile stability of such electronic ground states in 2D materials.

Novel Braceletlike BiSbX3 (X = S, Se) Monolayers with an In-Plane Negative Poisson's Ratio and Anisotropic Photoelectric Properties.

In this work, we predict two novel two-dimensional (2D) auxetic materials, BiSbX3 (X = S, Se) monolayers, through first-principles calculations. Attributed to their special braceletlike structure, the in-plane negative Poisson's ratio (NPR) of BiSbS3 and BiSbSe3 monolayers are as high as -0.25 and -0.26, respectively. The phonon dispersion calculations, ab initio molecular dynamics simulations, and elastic constants calculations demonstrate that these two monolayers possess excellent dynamic, thermal, and mechanical stabilities. The band gap values of BiSbS3 and BiSbSe3 calculated at the HSE level by considering the spin-orbit coupling (SOC) effect are 1.68 and 1.20 eV. The anisotropic carrier mobility and superior optical absorption indicate that they may shine in the next generation of electronic and optoelectronic devices. All of these discoveries not only enrich the types of auxetic materials but also provide a structural reference for designing new auxetic materials on the molecular level. Furthermore, they can provide theoretical guidance for future applications of BiSbX3 (X = S, Se) monolayers in various fields.

Theoretical investigations of novel Janus Pb2SSe monolayer as a potential multifunctional material for piezoelectric, photovoltaic, and thermoelectric applications.

Two-dimensional Janus nanomaterials, due to their unique electronic, optical, and piezoelectric characteristics resulting from the antisymmetric structures, exhibit great prospects in multifunctional energy application to alleviate the energy crisis. Monolayer Janus Pb2SSe, with a black phosphorus-like structure and an indirect band gap of 1.59 eV as well as high carrier mobility (526-2105 cm2 V-1 s-1), displays outstanding potentials in the energy conversion between nanomechanical energy, solar energy, waste heat, and electricity, which has been comprehensively studied utilizing DFT-based simulations. The research results reveal that monolayer Pb2SSe not only possesses giant in-plane piezoelectricity of d11 = 75.1 pm V-1 but also superhigh out-of-plane piezoelectric coefficients (d31 = 0.5 pm V-1 and d33 = 15.7 pm V-1). Meanwhile, by constructing Pb2SSe bilayers, the out-of-plane piezoelectric coefficients can be significantly enhanced (d31 = 19.2 pm V-1 and d33 = 194.7 pm V-1). In addition, owing to the small conduction band offset, suitable donor band gap and excellent light absorption capability in the Pb2SSe/SnSe (Pb2SSe/GeSe) heterostructure, the power conversion efficiencies were calculated to be up to 20.02% (Pb2SSe/SnSe) and 19.28% (Pb2SSe/GeSe), making it a promising candidate for solar energy collection. Furthermore, from the thermoelectric electron and phonon transport calculations, it can be found that the Pb2SSe monolayer is an n-type thermoelectric material with ultrahigh ZT = 2.19 (1.52) at room temperature, which can be traced back to its ultralow κL = 0.78 (0.99) W m-1 K-1, and superhigh PF = 10.18 (8.25) mW m-1 K-2 along the x(y) direction at the optimal doping concentration at 300 K. The abovementioned versatile characteristics in the Janus Pb2SSe monolayer, along with its comprehensive stabilities (energy, dynamic, thermal, and mechanical stabilities), highlight its potential in clean energy harvesting.

Highly adjustable piezoelectric properties in two-dimensional LiAlTe2by strain and stacking.

Two-dimensional (2D) piezoelectric materials have attracted wide attention because they are of great significance to the composition of piezoelectric nanogenerators. In this work, we have systematically studied the piezoelectric properties of 2D LiAlTe2by using the first-principles calculation and found the 2D LiAlTe2monolayer exhibits both large in-plane piezoelectric coefficientd11(3.73 pm V-1) and out-of-plane piezoelectric coefficientd31(0.97 pm V-1). Moreover, the piezoelectric coefficients of 2D LiAlTe2are highly tunable by strain and stacking. When different uniaxial strains are applied,d11changes dramatically, butd31changes little. When 2% stretching is applied to 2D LiAlTe2monolayer along thex-axis,d11reaches 7.80 pm V-1, which is twice as large as the previously reported 2D piezoelectric material MoS2. Both AA stacking and AB stacking can enhance the piezoelectric properties of 2D LiAlTe2, but they have different effects on in-plane and out-of-plane piezoelectric coefficients. AA stacking can greatly increased31but has little impact ond11. In the case of four-layer AA stacking, thed31reaches 3.32 pm V-1. AB stacking can both increased11andd31, butd11grows faster thand31as the number of layers increases. In the case of four-layer AB stacking,d11reaches 18.05 pm V-1. The excellent and highly tunable piezoelectric performance provides 2D LiAlTe2greater potential for the application of piezoelectric nano-generators and other micro-nano piezoelectric devices.

Highly variable chloroplast genome from two endangered Papaveraceae lithophytes Corydalis tomentella and Corydalis saxicola.

The increasingly wide application of chloroplast (cp) genome super-barcode in taxonomy and the recent breakthrough in cp genetic engineering make the development of new cp gene resources urgent and significant. Corydalis is recognized as the most genotypes complicated and taxonomically challenging plant taxa in Papaveraceae. However, there currently are few reports about cp genomes of the genus Corydalis. In this study, we sequenced four complete cp genomes of two endangered lithophytes Corydalis saxicola and Corydalis tomentella in Corydalis, conducted a comparison of these cp genomes among each other as well as with others of Papaveraceae. The cp genomes have a large genome size of 189,029-190,247 bp, possessing a quadripartite structure and with two highly expanded inverted repeat (IR) regions (length: 41,955-42,350 bp). Comparison between the cp genomes of C. tomentella, C. saxicola, and Papaveraceae species, five NADH dehydrogenase-like genes (ndhF, ndhD, ndhL, ndhG, and ndhE) with psaC, rpl32, ccsA, and trnL-UAG normally located in the SSC region have migrated to IRs, resulting in IR expansion and gene duplication. An up to 9 kb inversion involving five genes (rpl23, ycf2, ycf15, trnI-CAU, and trnL-CAA) was found within IR regions. The accD gene was found to be absent and the ycf1 gene has shifted from the IR/SSC border to the SSC region as a single copy. Phylogenetic analysis based on the sequences of common CDS showed that the genus Corydalis is quite distantly related to the other genera of Papaveraceae, it provided a new clue for recent advocacy to establish a separate Fumariaceae family. Our results revealed one special cp genome structure in Papaveraceae, provided a useful resources for classification of the genus Corydalis, and will be valuable for understanding Papaveraceae evolutionary relationships.

Monolayer Janus Te2Se-based gas sensor to detect SO2 and NOx: a first-principles study.

In this study, the adsorption of gas molecules, such as O2, NH3, CO, CO2, H2O, NOx (x = 1, 2) and SO2, on Janus Te2Se monolayer has been investigated by means of density functional theory (DFT) calculations. We show that Janus Te2Se monolayer is preferable for SO2 and NOx molecules with suitable adsorption strength and apparent charge transfers. We further calculated the current-voltage (I-V) curves using the nonequilibrium Green's function (NEGF) method. The transport feature exhibits distinct responses with a dramatic change of I-V curves before and after NOx (SO2) adsorption on Janus Te2Se. Thus, we predict that Janus Te2Se could be a promising candidate for SO2 and NOx sensors with high selectivity and sensitivity. Moreover, the effect of strain on the gas/substrate adsorption systems was also studied, implying that the strained Janus Te2Se monolayer could enhance the sensitivity and selectivity to SO2 and NO2. The adsorbed SO2 and NO2 on Janus Te2Se could escape by releasing the applied strain, which indicates that the capture process is reversible. Our study widens the application of Janus Te2Se not only as piezoelectric materials, but also as a potential gas sensor or capturer of SO2 and NOx with high sensitivity and selectivity.

C60 self-orientation on hexagonal boron nitride induced by intermolecular coupling.

A deep grasp of the properties of the interface between organic molecules and hexagonal boron nitride (h-BN) is essential for the full implementation of these two building blocks in the next generation of electronic devices. Here, using scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS), we report on the geometric and electronic features of C60 evaporated on a single layer of h-BN grown on a Rh(110) surface under ultra-high vacuum. Two different molecular assemblies of C60 on the h-BN/Rh(110) surface were observed. The first STM study at room temperature (RT) and at low temperatures (40 K) looked at the molecular orientation of C60 on a two-dimensional layered material. Intramolecular-resolution images demonstrate the existence of a phase transition of C60 over the h-BN/Rh(110) surface similar to that found on bulk solid C60. At RT molecules exhibit random orientations, while at 40 K such rotational disorder vanishes and they adopt a common orientation over the h-BN/Rh(110) surface. The decrease in thermal energy allows recognition between C60 molecules, and they become equally oriented in the configuration at which the van der Waals intermolecular interactions are optimized. Bias-dependent submolecular features obtained by means of high-resolution STM images are interpreted as the highest occupied and lowest unoccupied molecular orbitals. STS data showed that fullerenes are electronically decoupled from the substrate, with a negligible charge transfer effect if any. Finally, the very early stages of multilayer growth were also investigated.

9,9-Dimethylxanthene Derivatives with Room-Temperature Phosphorescence: Substituent Effects and Emissive Properties.

Room-temperature phosphorescence (RTP) emitters with ultralong lifetimes are emerging as attractive targets because of their potential applications in bioimaging, security, and other areas. But their development is limited by ambiguous mechanisms and poor understanding of the correlation of the molecular structure and RTP properties. Herein, different substituents on the 9,9-dimethylxanthene core (XCO) result in compounds with RTP lifetimes ranging from 52 to 601 ms, which are tunable by intermolecular interactions and molecular configurations. XCO-PiCl shows the most persistent RTP because of its reduced steric bulk and multiple sites of the 1-chloro-2-methylpropan-2-yl (PiCl) moiety for forming intermolecular interactions in the aggregated state. The substituent effects reported provide an efficient molecular design of organic RTP materials and establishes relationships among molecular structures, intermolecular interactions, and RTP properties.

Comparing chloroplast genomes of traditional Chinese herbs Schisandra sphenanthera and S. chinensis.

Objective: Schisandra sphenanthera and S. chinensis are the two important medicinal plants that have long been used under the names of "Nan-Wuweizi" and "Wuweizi", respectively. The misuse of "Nan-Wuweizi" and "Wuweizi" in herbal medical products calls for an accurate method to distinguish these herbs. Chloroplast (cp) genomes have been widely used in species delimitation and phylogeny due to their uniparental inheritance and lower substitution rates than that of the nuclear genomes. To develop more efficient DNA markers for distinguishing S. sphenanthera, S. chinensis, and the related species, we sequenced the cp genome of S. sphenanthera and compared it to that of S. chinensis. Methods: The cp genome of S. sphenanthera was sequenced at the Illumina HiSeq platform, and the reference-guided mapping of contigs was obtained with a de novo assembly procedure. Then, comparative analyses of the cp genomes of S. sphenanthera and S. chinensis were carried out. Results: The cp genome of S. sphenanthera was 146 853 bp in length and consisted of a large single copy (LSC) region of 95 627 bp, a small single copy (SSC) region of 18 292 bp, and a pair of inverted repeats (IR) of 16 467 bp. GC content was 39.6%. A total of 126 functional genes were predicted, of which 113 genes were unique, including 79 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Five tRNA, four protein-coding genes, and all rRNA were duplicated in the IR regions. There were 18 intron-containing genes, including six tRNA genes and 12 protein-coding genes. In addition, 45 SSRs were detected. The whole cp genome of S. sphenanthera was 123 bp longer than that of S. chinensis. A total of 474 SNPs and 97 InDels were identified. Five genetic regions with high levels of variation (Pi > 0.015), trnS-trnG, ccsA-ndhD, psbI-trnS, trnT-psbD and ndhF-rpl32 were revealed. Conclusion: We reported the cp genome of S. sphenanthera and revealed the SNPs and InDels between the cp genomes of S. sphenanthera and S. chinensis. This study shed light on the species identification and further phylogenetic study within the genus of Schisandra.

Large conformation shifts of Vibrio cholerae VqmA dimer in the absence of target DNA provide insight into DNA-binding mechanisms of LuxR-type receptors.

Quorum sensing regulates the biofilm formation and expression of virulence factors in Vibrio cholerae, an obligate human pathogen that continues to imperil human health. Cytoplasmic transcription factor VqmA is a LuxR-type receptor ubiquitous in the Vibrio genus and one vibriophage VP882 and plays an important role in V. cholerae pathogenicity. Here we presented the X-ray crystal structure of V. cholerae VqmA-DPO complex and compared it with the previously determined VqmA-DPO-DNA complex. To our knowledge, this is the first report on the crystal structures of the same LuxR-type receptor with two conformations of binding to DNA and not binding to DNA. Based on the results of structural analysis and biochemical assays, we revealed the secondary structure of the linker region between two function domains changed significantly, and DNA binding domains were covalently linked by a disulfide bond formed by the highly conserved Cys134. Besides, the distance between two DBD monomers became longer than that in DNA-binding conformation, and two α8 helixes underwent a large conformation shift. The results of the structure-function analyses presented here improve our understanding of the complex mechanisms in the conformational changes of LuxR-type receptors caused by DNA binding.

Crystal structures of phage NrS-1 N300-dNTPs-Mg2+ complex provide molecular mechanisms for substrate specificity.

A novel DNA polymerase from the deep-sea vent phage NrS-1, was characterized as a primase-polymerase (referred to as prim-pol), which works as a self-priming DNA polymerase to synthesize de novo long DNA strands. Functional research on the NrS-1 prim-pol illustrated that the N-terminal 300 residues (referred to as N300) have de novo synthesis activity similar to that of the full-length enzyme. Just like other prim-pols, NrS-1 prim-pol was able to initiate DNA synthesis, proficiently discriminating against ribonucleotides (NTPs), exclusively using deoxynucleotides (dNTPs). However, the structural basis for this discrimination is not well understood. Here, the three kinds of crystal structures of N300-dNTPs-Mg2+ complex were determined. These complex structures shared the identical steric architecture and hydrogen-bond interactions in the catalytic center. The results of biochemical studies indicated that R145 possibly plays an indispensable role in the primer extension. Mutagenesis and structural simulation showed that the backbone carboxyl group of Y146, as a potential sugar selector, was involved in steric clashing with the incoming 2'-OH group of NTPs. However, the mechanism of substrate discrimination probably was different from that of other prim-pols, according to the structural analyses and sequence comparison.