A TeZla micromixer for interrogating the early and broad folding landscape of G-quadruplex via multistage velocity descending.

Biomacromolecular folding kinetics involves fast folding events and broad timescales. Current techniques face limitations in either the required time resolution or the observation window. In this study, we developed the TeZla micromixer, integrating Tesla and Zigzag microstructures with a multistage velocity descending strategy. TeZla achieves a significant short mixing dead time (40 µs) and a wide time window covering four orders of magnitude (up to 300 ms). Using this unique micromixer, we explored the folding landscape of c-Myc G4 and its noncanonical-G4 derivatives with different loop lengths or G-vacancy sites. Our findings revealed that c-Myc can bypass folding intermediates and directly adopt a G4 structure in the cation-deficient buffer. Moreover, we found that the loop length and specific G-vacancy site could affect the folding pathway and significantly slow down the folding rates. These results were also cross-validated with real-time NMR and circular dichroism. In conclusion, TeZla represents a versatile tool for studying biomolecular folding kinetics, and our findings may ultimately contribute to the design of drugs targeting G4 structures.

Structural basis for high-affinity recognition of aflatoxin B1 by a DNA aptamer.

The 26-mer DNA aptamer (AF26) that specifically binds aflatoxin B1 (AFB1) with nM-level high affinity is rare among hundreds of aptamers for small molecules. Despite its predicted stem-loop structure, the molecular basis of its high-affinity recognition of AFB1 remains unknown. Here, we present the first high-resolution nuclear magnetic resonance structure of AFB1-AF26 aptamer complex in solution. AFB1 binds to the 16-residue loop region of the aptamer, inducing it to fold into a compact structure through the assembly of two bulges and one hairpin structure. AFB1 is tightly enclosed within a cavity formed by the bulges and hairpin, held in a place between the G·C base pair, G·G·C triple and multiple T bases, mainly through strong π-π stacking, hydrophobic and donor atom-π interactions, respectively. We further revealed the mechanism of the aptamer in recognizing AFB1 and its analogue AFG1 with only one-atom difference and introduced a single base mutation at the binding site of the aptamer to increase the discrimination between AFB1 and AFG1 based on the structural insights. This research provides an important structural basis for understanding high-affinity recognition of the aptamer, and for further aptamer engineering, modification and applications.

19F Nuclear Magnetic Resonance Fingerprinting Technique for Identifying and Quantifying G-Quadruplex Topology in Human Telomeric Overhangs.

G-quadruplexes (G4s) are noncanonical nucleic acid secondary structures with diverse topological features and biological roles. Human telomeric (Htelo) overhangs consisting of TTAGGG repeats can fold into G4s that adopt different topologies under physiological conditions. These G4s are potential targets for anticancer drugs. Despite intensive research, the existence and topology of G4s at Htelo overhangs in vivo are still unclear because there is no method to distinguish and quantify the topology of Htelo overhangs with native lengths that can form more than three tandem G4s in living cells. Herein, we present a novel 19F chemical shift fingerprinting technique to identify and quantify the topology of the Htelo overhangs up to five G-quadruplexes (G4s) and 120 nucleotides long both in vitro and in living cells. Our results show that longer overhang sequences tend to form stable G4s at the 5'- and 3'-ends, while the interior G4s are dynamic and "sliding" along the sequence, with TTA or 1-3 TTAGGG repeats as a linker. Each G4 in the longer overhang is conformationally heterogeneous, but the predominant ones are hybrid-2, two- or three-tetrad antiparallel, and hybrid-1 at the 5'-terminal, interior, and 3'-terminal, respectively. Additionally, we observed a distinct behavior of different lengths of telomeric sequences in living cells, suggesting that the overhang length and protein accessibility are related to its function. This technique provides a powerful tool for quickly identifying the folding topology and relative population of long Htelo overhangs, which may provide valuable insights into telomere functionality and be beneficial for structure-based anticancer drug development targeting G4s.

Real-Time Observation of Conformational Changes and Translocation of Endogenous Cytochrome c within Intact Mitochondria.

Cytochrome c (cyt c) is a multifunctional protein with varying conformations. However, the conformation of cyt c in its native environment, mitochondria, is still unclear. Here, we applied NMR spectroscopy to investigate the conformation and location of endogenous cyt c within intact mitochondria at natural isotopic abundance, mainly using widespread methyl groups as probes. By monitoring time-dependent chemical shift perturbations, we observed that most cyt c is located in the inner mitochondrial membrane and partially unfolded, which is distinct from its native conformation in solution. When suffering oxidative stress, cyt c underwent oxidative modifications due to increasing reactive oxygen species (ROS), weakening electrostatic interactions with the membrane, and gradually translocating into the inner membrane spaces of mitochondria. Meanwhile, the lethality of oxidatively modified cyt c to cells was reduced compared with normal cyt c. Our findings significantly improve the understanding of the molecular mechanisms underlying the regulation of ROS by cyt c in mitochondria. Moreover, it highlights the potential of NMR to monitor high-concentration molecules at a natural isotopic abundance within intact cells or organelles.

Short and long range 2D 15N-15N NMR correlations among peptide groups by novel solid state dipolar mixing schemes.

A recently developed homonuclear dipolar recoupling scheme, Adiabatic Linearly FREquency Swept reCOupling (AL FRESCO), was applied to record two-dimensional (2D) 15N-15N correlations on uniformly 15N-labeled GB1 powders. A major feature exploited in these 15N-15N correlations was AL FRESCO's remarkably low RF power demands, which enabled seconds-long mixing schemes when establishing direct correlations. These 15N-15N mixing schemes proved efficient regardless of the magic-angle spinning (MAS) rate and, being nearly free from dipolar truncation effects, they enabled the detection of long-range, weak dipolar couplings, even in the presence of strong short-range dipolar couplings. This led to a connectivity information that was significantly better than that obtained with spontaneously proton-driven, 15N spin-diffusion experiments. An indirect approach producing long-range 15N-15N correlations was also tested, relying on short (ms-long) 1HN-1HN mixings schemes while applying AL FRESCO chirped pulses along the 15N channel. These indirect mixing schemes produced numerous long-distance Ni-Ni±n (n = 2 - 5) correlations, that might be useful for characterizing three-dimensional arrangements in proteins. Once again, these AL FRESCO mediated experiments proved more informative than variants based on spin-diffusion-based 1HN-1HN counterparts.

Targeting New Functions and Applications of Bacterial Two-component Systems.

Two-component signal transduction systems (TCSs) are regulatory systems widely distributed in eubacteria, archaea, and a few eukaryotic organisms, but not in mammalian cells. A typical TCS consists of a histidine kinase and a response regulator protein. Functional and mechanistic studies on different TCSs have greatly advanced the understanding of cellular phosphotransfer signal transduction mechanisms. In this concept paper, we focus on the His-Asp phosphotransfer mechanism, the ATP synthesis function, antimicrobial drug design, cellular biosensors design, and protein allostery mechanisms based on recent TCS investigations to inspire new applications and future research perspectives.

An efficient method for detecting membrane protein oligomerization and complex using 05SAR-PAGE.

Oligomerization is an important feature of proteins, which gives a defined quaternary structure to complete the biological functions. Although frequently observed in membrane proteins, characterizing the oligomerization state remains complicated and time-consuming. In this study, 0.05% (w/v) sarkosyl-polyacrylamide gel electrophoresis (05SAR-PAGE) was used to identify the oligomer states of the membrane proteins CpxA, EnvZ, and Ma-Mscl with high sensitivity. Furthermore, two-dimensional electrophoresis (05SAR/sodium dodecyl sulfate-PAGE) combined with western blotting and liquid chromatography-tandem mass spectrometry was successfully applied to study the complex of CpxA/OmpA in cell lysate. The results indicated that 05SAR-PAGE is an efficient, economical, and practical gel method that can be widely used for the identification of membrane protein oligomerization and the analysis of weak protein interactions.

In-Cell 19F†NMR of Proteins: Recent Progress and Future Opportunities.

In vitro, 19F NMR methodology is preferably selected as a complementary and straightforward method for unveiling the conformations, dynamics, and interactions of biological molecules. Its effectiveness in vivo has seen continuous improvement, addressing challenges faced by conventional heteronuclear NMR experiments on structured proteins, such as severe line broadening, low signal-to-noise ratio, and background signals. Herein, we summarize the distinctive advantages of 19F NMR, along with recent progress in sample preparation and applications within the realm of in-cell NMR. Additionally, we offer insights into the future directions and prospects of this methodology based on our understanding.

KNa2Lu(BO3)2: A Rare-Earth Borate Crystal Characterized by an Enhanced Birefringence and Wide Ultraviolet Transparency Range.

Borate materials are of significant interest due to their versatile structural configuration and competitive ultraviolet (UV) transparency range. In this study, we present a novel rare-earth borate crystal, KNa2Lu(BO3)2, synthesized for the first time through a facile spontaneous crystallization method. It adopts the centrosymmetric space group Pnma (no. 62) and yields a unique three-dimensional (3D) structural network formed by isolated [BO3] plane triangles and distorted [LuO7] polyhedra. This compound displays excellent thermal stability up to ∼990 °C, demonstrating a favorable congruent melting nature. Moreover, KNa2Lu(BO3)2 achieves a notably short UV absorption cutoff at approximately 204 nm, yielding a large band gap of 5.58 eV. Remarkably, it showcases an enlarged birefringence of 0.044 at 1064 nm, implying its potential as a birefringent material. Moreover, density functional theory calculations demonstrate that the optical characteristics are predominantly influenced by fundamental building blocks [BO3] triangles and distorted [LuO7] polyhedra. Our findings demonstrate the potential of KNa2Lu(BO3)2 in the development of a birefringent candidate and enrich the structural chemistry of rare-earth-based borates.

Li13YGe4O16: A Mid-infrared Rare-Earth Germanate Nonlinear Optical Crystal Featuring a Broad Transmission Range and an Enlarged Band Gap.

Germanate is garnering increasing attention in the field of optoelectronics owing to its competitive optical transparency and robust stability. Herein, a novel lithium-rich rare-earth germanate, Li13YGe4O16, was fabricated for the first time using a high-temperature solution approach. This compound adopts the asymmetric space group Cmc21 (no. 36), characterized by isolated [YO6] and [GeO4] structural motifs with Li+ cations located in the channel. Notably, Li13YGe4O16 presents a short ultraviolet cutoff edge at 240 nm, indicative of an enlarged band gap of 4.96 eV and showcases a wide mid-infrared transmission region exceeding 6.0 µm. Moreover, Li13YGe4O16 features exceptional thermal stability and moderate second harmonic generation (SHG) intensity. Additionally, a theoretical analysis suggests that the distorted [YO6] octahedra. [GeO4] and [LiO4] tetrahedra play a significant role in the optical activities of Li13YGe4O16. These attributes endow Li13YGe4O16 with the potential to serve as a new mid-IR nonlinear optical (NLO) crystal and enrich the structural chemistry of germanates.

NMR spectroscopy for metabolomics in the living system: recent progress and future challenges.

Metabolism is a fundamental process that underlies human health and diseases. Nuclear magnetic resonance (NMR) techniques offer a powerful approach to identify metabolic processes and track the flux of metabolites at the molecular level in living systems. An in vitro study through in-cell NMR tracks metabolites in real time and investigates protein structures and dynamics in a state close to their most natural environment. This technique characterizes metabolites and proteins involved in metabolic pathways in prokaryotic and eukaryotic cells. In vivo magnetic resonance spectroscopy (MRS) enables whole-organism metabolic monitoring by visualizing the spatial distribution of metabolites and targeted proteins. One limitation of these NMR techniques is the sensitivity, for which a possible improved approach is through isotopic enrichment or hyperpolarization methods, including dynamic nuclear polarization (DNP) and parahydrogen-induced polarization (PHIP). DNP involves the transfer of high polarization from electronic spins of radicals to surrounding nuclear spins for signal enhancements, allowing the detection of low-abundance metabolites and real-time monitoring of metabolic activities. PHIP enables the transfer of nuclear spin polarization from parahydrogen to other nuclei for signal enhancements, particularly in proton NMR, and has been applied in studies of enzymatic reactions and cell signaling. This review provides an overview of in-cell NMR, in vivo MRS, and hyperpolarization techniques, highlighting their applications in metabolic studies and discussing challenges and future perspectives.

The intracellular environment affects protein-protein interactions.

Protein-protein interactions are essential for life but rarely thermodynamically quantified in living cells. In vitro efforts show that protein complex stability is modulated by high concentrations of cosolutes, including synthetic polymers, proteins, and cell lysates via a combination of hard-core repulsions and chemical interactions. We quantified the stability of a model protein complex, the A34F GB1 homodimer, in buffer, Escherichia coli cells and Xenopus laevis oocytes. The complex is more stable in cells than in buffer and more stable in oocytes than E. coli Studies of several variants show that increasing the negative charge on the homodimer surface increases stability in cells. These data, taken together with the fact that oocytes are less crowded than E. coli cells, lead to the conclusion that chemical interactions are more important than hard-core repulsions under physiological conditions, a conclusion also gleaned from studies of protein stability in cells. Our studies have implications for understanding how promiscuous-and specific-interactions coherently evolve for a protein to properly function in the crowded cellular environment.

An ATP "Synthase" Derived from a Single Structural Domain of Bacterial Histidine Kinase.

ATP (adenosine triphosphate) is a vital energy source for living organisms, and its biosynthesis and precise concentration regulation often depend on macromolecular machinery composed of protein complexes or complicated multidomain proteins. We have identified a single-domain protein HK853CA derived from bacterial histidine kinases (HK) that can catalyze ATP synthesis efficiently. Here, we explored the reaction mechanism and multiple factors that influence this catalysis through a combination of experimental techniques and molecular simulations. Moreover, we optimized its enzymatic activity and applied it as an ATP replenishment machinery to other ATP-dependent systems. Our results broaden the understanding of ATP biosynthesis and show that the single CA domain can be applied as a new biomolecular catalyst used for ATP supply.

Tailored Synthesis of Two Metal Borates KSrM3B2O9 (M = Al and Ga) Exhibiting Wide Ultraviolet Transparency.

Borate materials continue to command considerable attention due to their remarkable capacity for applications in deep ultraviolet (UV) wavelengths. Herein, two new metal borates KSrM3B2O9 (M = Al and Ga) were extracted via the application of flux techniques. These two crystals adopt a centrosymmetric space group P21/c (no. 14), showcasing a layered structural configuration composed of isolated [BO3] plane triangles and [AlO4]/[GaO4] tetrahedra. Thermal analysis revealed that KSrM3B2O9 (M = Al and Ga) exhibits an incongruent nature and possesses good thermal stability up to 1083 and 983 °C, respectively. Notably, these compounds display a short UV-transmission cutoff edge, approximately around 194 and 200 nm, accompanied by band gaps of 5.47 and 4.83 eV, respectively. Furthermore, KSrM3B2O9 (M = Al and Ga) demonstrates a moderate optical birefringence of 0.026 and 0.025, respectively. Additionally, first-principles calculations were employed to shed light on the intricate interplay between the structure and properties of these compounds.

Rational Design of a Niobium Tellurite Crystal Nb2Te3O11 Exhibiting Good Overall Infrared NLO Performance by Structural Genetic Engineering.

Nonlinear optical (NLO) materials have aroused increasing interest owing to their promising applications in optoelectronic technologies. Herein, we present the synthesis of an acentric niobium tellurite crystal, Nb2Te3O11, extracted via a spontaneous crystallization approach. It adopts a unique three-dimensional (3D) structure constructed by the distorted [TeO3], [TeO4], and [NbO6] fundamental building units. The title compound undergoes incongruent melting at approximately 807 °C. Optical characterizations demonstrate that Nb2Te3O11 possesses an extended transparency window beyond 5 µm, along with a large band gap value of 3.1 eV. Moreover, the as-synthesized Nb2Te3O11 displays an appreciable second-harmonic generation (SHG) response of 2 × KDP and a notable birefringence of 0.11 under 1064 nm for achieving phase-matching. In addition, theoretical calculation investigations suggest that the intriguing optical properties are ascribed to the cooperative effect of three types of NLO-active motifs: [TeO3] pyramids, [TeO4] seesaws, and [NbO6] octahedra. These attributes provide new functional insights into Nb2Te3O11 and enrich the family of NLO crystals in the mid-infrared region.

Visualizing Proteins in Human Cells at Near-Physiological Concentrations with Sensitive 19 F NMR Chemical Tags.

In-cell NMR spectroscopy is an effective tool for observing proteins at atomic resolution in their native cellular environment. However, its utility is limited by its low sensitivity and the extensive line broadening caused by nonspecific interactions in the cells, which is even more pronounced in human cells due to the difficulty of overexpressing or delivering high concentrations of isotopically labeled proteins. Here, we present a high-sensitivity tag (wPSP-6F) containing two trifluoromethyl groups that can efficiently label globular proteins with molecular weights in the 6-40 kDa range under mild conditions. This tag allowed us to detect globular proteins in human cells at concentrations as low as 1.0 µM, which would not have been achievable with 15 N or 3-fluorotyrosine labeling. Moreover, we detected conformational changes and interactions of proteins in the cellular environment. The new sensitive 19 F NMR tag may significantly expand the scope of protein NMR in human cells.

An NIR Fluorescence Turn-on and MRl Bimodal Probe for Concurrent Real-time in vivo Sensing and Labeling of ß-Galactosidase.

To realize sensing and labeling biomarkers is quite challenging in terms of designing multimodal imaging probes. In this study, we developed a novel ß-galactosidase (ß-gal) activated bimodal imaging probe that combines near-infrared (NIR) fluorescence and magnetic resonance imaging (MRI) to enable real-time visualization of activity in living organisms. Upon ß-gal activation, Gal-Cy-Gd-1 exhibits a remarkable 42-fold increase in NIR fluorescence intensity at 717 nm, allowing covalent labeling of adjacent target enzymes or proteins and avoiding molecular escape to promote probe accumulation at the tumor site. This fluorescence reaction enhances the longitudinal relaxivity by approximately 1.9 times, facilitating high-resolution MRI. The unique features of Gal-Cy-Gd-1 enable real-time and precise visualization of ß-gal activity in live tumor cells and mice. The probe's utilization aids in identifying in situ ovarian tumors, offering valuable assistance in the precise removal of tumor tissue during surgical procedures in mice. The fusion of NIR fluorescence and MRI activation through self-immobilizing target enzymes or proteins provides a robust approach for visualizing ß-gal activity. Moreover, this approach sets the groundwork for developing other activatable bimodal probes, allowing real-time in vivo imaging of enzyme activity and localization.

Electrocatalytic Urea Synthesis with 63.5 % Faradaic Efficiency and 100 % N-Selectivity via One-step C-N coupling.

Electrocatalytic urea synthesis via coupling N2 and CO2 provides an effective route to mitigate energy crisis and close carbon footprint. However, the difficulty on breaking N≡N is the main reason that caused low efficiencies for both electrocatalytic NH3 and urea synthesis, which is the bottleneck restricting their industrial applications. Herein, a new mechanism to overcome the inert of the nitrogen molecule was proposed by elongating N≡N instead of breaking N≡N to realize one-step C-N coupling in the process for urea production. We constructed a Zn-Mn diatomic catalyst with axial chloride coordination, Zn-Mn sites display high tolerance to CO poisoning and the Faradaic efficiency can even be increased to 63.5 %, which is the highest value that has ever been reported. More importantly, negligible N≡N bond breakage effectively avoids the generation of ammonia as intermediates, therefore, the N-selectivity in the co-electrocatalytic system reaches100 % for urea synthesis. The previous cognition that electrocatalysts for urea synthesis must possess ammonia synthesis activity has been broken. Isotope-labelled measurements and Operando synchrotron-radiation Fourier transform infrared spectroscopy validate that activation of N-N triple bond and nitrogen fixation activity arise from the one-step C-N coupling process of CO species with adsorbed N2 molecules.

Structural Insights into the Mechanism of High-Affinity Binding of Ochratoxin A by a DNA Aptamer.

A 36-mer guanine (G)-rich DNA aptamer (OBA36) is able to distinguish one atomic difference between ochratoxin analogues A (OTA) and B (OTB), showing prominent recognition specificity and affinity among hundreds of aptamers for small molecules. Why OBA36 has >100-fold higher binding affinity to OTA than OTB remains a long-standing question due to the lack of high-resolution structure. Here we report the solution NMR structure of the aptamer-OTA complex. It was found that OTA binding induces the aptamer to fold into a well-defined unique duplex-quadruplex structural scaffold stabilized by Mg2+ and Na+ ions. OTA does not directly interact with the G-quadruplex, but specifically binds at the junction between the double helix and G-quadruplex through π-π stacking, halogen bonding (X-bond), and hydrophobic interaction. OTB has the same binding site as OTA but lacks the X-bond. The strong X-bond formed between the chlorine atom of OTA and the aromatic ring of C5 is the key to discriminating the strong binding toward OTA. The present research contributes to a deeper insight of aptamer molecular recognition, reveals structural basis of the high-affinity binding of aptamers, and provides a foundation for further aptamer engineering and applications.

Photoactivated Nanohybrid for Dual-Nuclei MR/US/PA Multimodal-Guided Photothermal Therapy.

Nanohybrids have gained immense popularity for the diagnosis and chemotherapy of lung cancer for their excellent biocompatibility, biodegradability, and targeting ability. However, most of them suffer from limited imaging information, low tumor-to-background ratios, and multidrug resistance, limiting their potential clinical application. Herein, we engineered a photoresponsive nanohybrid by assembling polypyrrole@bovine serum albumin (PPy@BSA) encapsulating perfluoropentane (PFP)/129Xe for selective magnetic resonance (MR)/ultrasonic (US)/photoacoustic (PA) trimodal imaging and photothermal therapy of lung cancer, overcoming these drawbacks of single imaging modality and chemotherapy. The nanohybrid exhibited superior US, PA, and MR multimodal imaging performance for lung cancer detection. The high sensitivity of the nanohybrid to near-infrared light (NIR) resulted in a rapid increase in temperature in a low-intensity laser state, which initiated the phase transition of liquid PFP into the gas. The ultrasound signal inside the tumor, which is almost zero initially, is dramatically increased. Beyond this, it led to the complete depression of 19F/129Xe Hyper-CEST (chemical exchange saturation transfer) MRI during laser irradiation, which can precisely locate lung cancer. In vitro and in vivo results of the nanohybrid exhibited a successful therapeutic effect on lung cancer. Under the guidance of imaging results, a sound effect of photothermal therapy (PTT) for lung cancer was achieved. We expect this nanohybrid and photosensitive behavior will be helpful as fundamental tools to decipher lung cancer in an earlier stage through trimodality imaging methods.