Cis-trans Research Articles

Stereoselective Reaction Enabling Simultaneous Analysis of Carbon-Carbon Double-Bond Configuration and the Position of Monounsaturated Fatty Acids through UHPLC-ESI-MRM-MS.

Monounsaturated fatty acids (MUFA) are an important class of nutrients and are involved in lipid metabolism. The positions of the C=C bond and cis-trans isomerism have a significant influence on their physiological activity. However, simultaneously detecting these two structural properties has been challenging due to multiple isomers of MUFA. In this study, we developed a method that involved an N-aminophthalimide (PhthNH2) derivatization of the C=C bond in MUFA, followed by analysis using ultrahigh-performance liquid chromatography-electrospray ionization-multiple reaction monitoring mass spectrometry (UHPLC-ESI-MRM-MS) technology to achieve analysis of cis-trans isomers and positional isomers of the C=C bond. The derivatives of cis-trans isomers of the C=C bond were well separated in UHPLC, and their corresponding C=C bond positions were deduced from characteristic fragment ions in tandem mass spectrometry. With our method, we found MUFA with different double-bond positions and cis-trans isomers in several samples, including mouse kidney, butter, etc., achieving qualitative analysis and relative quantitation. This method is expected to be applied by more researchers in lipidomics studies in the future.

Unraveling the Mechanism and Influence of Auxiliary Ligands on the Isomerization of Neutral [P,O]-Chelated Nickel Complexes for Olefin Polymerization.

The copolymerization of ethylene with polar monomers presents a significant challenge. While palladium catalysts have shown promise, nickel catalysts are more economical but suffer from poor activity. Previous studies suggest that the isomerization step involved in the nickel-catalyzed polymerization may influence the catalyst activities. Herein, we explore the isomerization mechanisms of two phosphine-phenoxide-ligated catalysts using density functional theory (DFT) studies. We found that out of dissociative, tetrahedral, and associative mechanisms, the associative mechanism is the likeliest, with a pendant methoxy oxygen atom from the ligand to fulfill the fifth coordination site on nickel before Berry pseudorotation. The effect of varying auxiliary ligands on the activation barrier heights was also investigated and found that electron-releasing alkyl groups on substituted pyridine ligands have diminished electronic influence on pseudorotational barriers, but if present at the ortho-positions, will elevate the barriers due to larger steric influences. The electron-withdrawing groups on the ligand result in weaker ligand binding and lower pseudorotational barriers. These insights into the mechanisms of cis-trans isomerization and auxiliary ligand effects may offer valuable guidance for optimizing catalyst performance in copolymerization processes by lowering the barrier of isomerization by fine-tuning the steric and electronic influences of auxiliary ligands and enhancing overall copolymerization efficiency.

Conformational dynamics in specialized C2H2 zinc finger domains enable zinc-responsive gene repression in S. pombe.

Loz1 is a zinc-responsive transcription factor in fission yeast that maintains cellular zinc homeostasis by repressing the expression of genes required for zinc uptake in high zinc conditions. Previous deletion analysis of Loz1 found a region containing two tandem C2H2 zinc-fingers and an upstream "accessory domain" rich in histidine, lysine, and arginine residues to be sufficient for zinc-dependent DNA binding and gene repression. Here we report unexpected biophysical properties of this pair of seemingly classical C2H2 zinc fingers. Isothermal titration calorimetry and NMR spectroscopy reveal two distinct zinc binding events localized to the zinc fingers. NMR spectra reveal complex dynamic behavior in this zinc-responsive region spanning time scales from fast 10-12-10-10 to slow >100 s. Slow exchange due to cis-trans isomerization of the TGERP linker results in the doubling of many signals in the protein. Conformational exchange on the 10-3 s timescale throughout the first zinc finger distinguishes it from the second and is linked to a weaker affinity for zinc. These findings reveal a mechanism of zinc sensing by Loz1 and illuminate how the protein's rough free-energy landscape enables zinc sensing, DNA binding and regulated gene expression.

Calcium-binding protein CALU-1 is essential for proper collagen formation in Caenorhabditis elegans

Collagen, a major component of the extracellular matrix, is crucial for the structural integrity of the Caenorhabditis elegans cuticle. While several proteins involved in collagen biosynthesis have been identified, the complete regulatory network remains unclear. This study investigates the role of CALU-1, an ER-resident calcium-binding protein, in cuticle collagen formation and maintenance. We employed genetic analyses, including the generation of single and double mutants, scanning electron microscopy, and transcriptome profiling to characterize CALU-1 function. Our results demonstrate that CALU-1 is essential for proper cuticle structure, including annuli, furrows, and alae formation. Synthetic lethality was observed between calu-1 and dpy-18 (encoding a prolyl 4-hydroxylase subunit) mutations, while double mutants of calu-1 with peptidyl-prolyl cis–trans isomerase (PPIase) genes exhibited exacerbated phenotypes. CALU-1 deficiency led to altered collagen stability, increased cuticle permeability, and differential expression of stress response genes similar to collagen mutants. We conclude that CALU-1 plays a critical role in regulating collagen biosynthesis, possibly by modulating the ER environment to optimize the function of collagen-modifying enzymes. These findings provide new insights into the complex regulation of extracellular matrix formation in C. elegans, with potential implications for understanding related processes in other organisms.

OXCT1 succinylation and activation by SUCLA2 promotes ketolysis and liver tumor growth.

Ketone bodies generated in hepatocytes in the adult liver are used for nonhepatic tissues as an energy source. However, ketolysis is reactivated in hepatocellular carcinoma (HCC) cells with largely unelucidated mechanisms. Here, we demonstrate that 3-oxoacid CoA-transferase 1 (OXCT1), a rate-limiting enzyme in ketolysis, interacts with SUCLA2 upon IGF1 stimulation in HCC cells. This interaction results from ERK2-mediated SUCLA2 S124 phosphorylation and subsequent PIN1-mediated cis-trans isomerization of SUCLA2. OXCT1-associated SUCLA2 generates succinyl-CoA, which not only serves as a substrate for OXCT1 but also directly succinylates OXCT1 at K421 and activates OXCT1. SUCLA2-regulated OXCT1 activation substantially enhances ketolysis, HCC cell proliferation, and tumor growth in mice. Notably, treatment with acetohydroxamic acid, an OXCT1 inhibitor used clinically for urinary infection, inhibits liver tumor growth in mice and significantly enhances lenvatinib therapy. Our findings highlight the role of SUCLA2-coupled regulation of OXCT1 succinylation in ketolysis and unveil an unprecedented strategy for treating HCC by interrupting ketolysis.

Reversible Isomerization of Stiff-Stilbene by an Oriented External Electric Field.

Understanding and effectively controlling molecular conformational changes are essential for developing responsive and dynamic molecular systems. Here, we report that an oriented external electric field (OEEF) is an effective catalyst for the cis-trans isomerization of stiff-stilbene, a key component of overcrowded alkene-based rotary motors. This reversible isomerization occurs under ambient conditions, is free from side reactions, and has been verified using ultraperformance liquid chromatography and UV-vis absorption spectroscopy. Low electric field promotes cis-to-trans conversion, and high electric field enables the reverse trans-to-cis process, demonstrating the precise reaction control through electric field manipulation. Density functional theory calculations reveal the mechanism of the electric-field-catalyzed cis-trans carbon-carbon double bond isomerization. Our findings provide a novel perspective on constructing OEEF-catalyzed, reversible molecular systems and pave the way for fully electrically driven artificial molecular machines.

The Role of Light Irradiation and Dendrimer Generation in Directing Electrostatic Self-Assembly.

pH-responsive polyamidoamine (PAMAM) dendrimers are used as well-defined building blocks to design light-switchable nano-assemblies in solution. The complex interplay between the photoresponsive di-anionic azo dye Acid Yellow 38 (AY38) and the cationic PAMAM dendrimers of different generations is presented in this study. Electrostatic self-assembly involving secondary dipole-dipole interactions provides well-defined assemblies within a broad size range (10 nm-1 μm) with various shapes. The size and shape of these assemblies were determined using dynamic and static light scattering (DLS/SLS) and small-angle neutron scattering (SANS); ζ-potential measurements were performed to elucidate the charge characteristics, revealing the effective surface charge density of the nano-objects as an important parameter in the size and shape control. UV-vis spectroscopy and isothermal titration calorimetry (ITC) were employed to investigate the interaction on a molecular level and from a thermodynamic point of view. The results show that the amount of isomerized cis dye depends on the dendrimer generation because of a photoprotective effect through electrostatics for lower generations and through dipole-dipole interactions for higher generations; as the cis dye and trans dye bind with different strength, the amount of cis dye then again encodes the charge density and thereby the particle size and shape.

Tracking the Geometric and Positional Isomerization of Lipid C═C Bonds in the Bacterial Stress Responses by Mass Spectrometry.

The position and configuration of the C═C bond have a significant impact on the spatial conformation of unsaturated lipids, which subsequently affects their biological functions. Double bond isomerization of lipids is an important mechanism of bacterial stress response, but its in-depth mechanistic study still lacks effective analytical tools. Here, we developed a visible-light-activated dual-pathway reaction system that enables simultaneous [2 + 2] cycloaddition and catalytic cis-trans isomerization of the C═C bond of unsaturated lipids via directly excited anthraquinone radicals. Density functional theory calculations revealed the oxygen radical addition transition state and the addition-elimination isomerization mechanism of the reaction. A full-dimensional resolution method for C═C bond position and configuration was developed based on the bifunctional reaction and liquid chromatography-mass spectrometry. This method was then applied to the study of bacterial environmental stress response mechanisms. The C═C bond cis-trans and positional isomerization patterns of Pseudomonas membrane lipids under temperature stress were discovered, and the effect of temperature stress on fatty acid biosynthesis was also revealed. This study not only provides an effective tool and key information for the study of bacterial stress response mechanisms, but also enriches the toolbox of visible light chemical reactions.

Influence of cis–trans isomerization induced by photoexcitation on the antioxidant properties of piceatannol and its derivatives

Influence of cis–trans isomerization induced by photoexcitation on the antioxidant properties of piceatannol and its derivatives

CC bond enables difluorideboron β-diketonate derivatives with high contrast mechanoresponsive luminescence for reversible writing and information encryption

CC bond cis–trans isomerization and “head-to-head” arrangement induced in high-contrast mechanoresponsive luminescence.

Synthesis, Characteristics and Thermally Induced Self-Assembly of Silicon-Based Thermo/Photo-Responsive Block Copolymers Prepared from Monomer Bearing Paired Side-Chain Azo Mesogens Using RAFT Process

Novel silicon-based liquid crystalline (LC) monomer (CASPA) and corresponding Poly(MMA)-b-Poly(CASPA) diblock copolymers (DBCs) containing symmetric azobenzene mesogens in the side chain were successfully synthesized by coupling reaction and reversible addition-fragmentation chain transfer (RAFT) polymerization, respectively. Block copolymerization by RAFT proceeded with well-controlled manner in anisole solution involving new CASPA monomer, Poly(MMA)-RAFT macroinitiator and AIBN initiator, yielding Poly(MMA)-b-Poly(CASPA) DBCs with excellent control over molecular weights (Mw/Mn ≤ 1.39) and compositions. Chemical structures and properties of CASPA and Poly(MMA)-b-Poly(CASPA) were extensively studied using 1H NMR, FTIR, GPC, DSC, POM, AFM and GISAXS. The CASPA exhibited enantiotropic liquid crystallinity with nematic four-brush schlieren texture, while DBCs showed monotropic liquid crystallinity with batonnet textures of smectic A phase. All DBC films exhibited photochemical trans-cis isomerization and photoinduced phase transition from mesophase to isotropic phase under UV irradiation. Morphologies of DBC thin films under thermal annealing depended on volume ratio of building LC block relative to Poly(MMA) segment, DBC-2 containing approximately equal block volume fractions self-assembled into lamellar nanostructure with domain-spacing of 34 nm, whereas DBC-3 and DBC-4 possessing higher LC contents (65 wt% and 72 wt%) formed highly ordered hexagonal cylindrical nanostructures with domain-spacing ranging from 37 to 39 nm as evidence by AFM and GI-SAXS, conforming with the self-consistent field theory.

Precise Light-Driven Polarity of Stationary Phase for Regulating Gradient Separation of Liquid Chromatography.

Generally, the traditional stationary phase for liquid chromatography is the key part, but with an in situ immutable property, leading to many separation limitations. Based on the former exploration of photosensitive gas chromatography, we successfully prepared a photosensitive monolithic capillary silica column with high light transmission, taking advantage of the reversible cis-trans isomerism of azobenzene. And the cis-trans isomerism has launched an effective, reversible, and precise control on the liquid chromatographic retention behavior just by photoinduction according to the theoretical basis of a good correlation between photoinduction time, trans-azobenzene ratio, and chromatographic retention factor (k) (R2 > 0.9586). In this system, the plausible control mechanism of stationary phase's polarity is the synergistic effect of the self-molecular polarity difference and the occupation (or release) of polar groups on the stationary phase surface by cis-trans isomerism. Furthermore, a "light control-time ratio cycle" strategy was first reported to maintain an arbitrary ratio of trans-azobenzene corresponding to the polarity gradient of the stationary phase during the whole chromatographic separation process, which is verified by a close correlation of the retention time of the targets and the ratio of light-controlled time (R2 > 0.9977). The "gradient elution" of the targets was also surprisingly realized due to the gradient regulation of stationary phase's polarity by the programmatic control of alternate light induction and time ratio. This work further advances the practical significance of photosensitive chromatography in "one column for multiple columns", even "one column for multidimensional chromatography", and truly provides research foundation for its development in the separation and analysis of complex biological samples.

Multiphase Janus Azobenzene Inverse Opal Membrane toward On-Demand Photocontrolled Motion.

Azobenzene actuators have generated extensive research investment in the field of soft robots, artificial muscles, etc., based on the typical photoresponsive trans-cis isomerization. However, it remains challenging to achieve multiphase actuation at the gas-liquid interface and liquid phase. To solve these problems, this paper demonstrated a simple fabrication method of a Janus azobenzene inverse opal membrane with one side having a polydomain azobenzene inverse opal structure and the other side having a monodomain bulk azobenzene polymer. The introduction of an inverse opal structure increases the interaction area between the liquid and polymer network. The proposed design can freely swim in any direction at the air-liquid interface based on the Marangoni effect or move forward in the liquid phase based on bubble propulsion under UV irradiation. This work is of great significance for the design and fabrication of multiphase photo actuators.

Accuracy of Reaction Coordinate Based Rate Theories for Modelling Chemical Reactions: Insights From the Thermal Isomerization in Retinal.

Modern potential energy surfaces have shifted attention to molecular simulations of chemical reactions. While various methods can estimate rate constants for conformational transitions in molecular dynamics simulations, their applicability to studying chemical reactions remains uncertain due to the high and sharp energy barriers and complex reaction coordinates involved. This study focuses on the thermal cis-trans isomerization in retinal, employing molecular simulations and comparing rate constant estimates based on one-dimensional rate theories with those based on sampling transitions and grid-based models for low-dimensional collective variable spaces. Even though each individual method to estimate the rate passes its quality tests, the rate constant estimates exhibit considerable disparities. Rate constant estimates based on one-dimensional reaction coordinates prove challenging to converge, even if the reaction coordinate is optimized. However, consistent estimates of the rate constant are achieved by sampling transitions and by multi-dimensional grid-based models.

Photochemical Control of Cell Division Using a Photoswitchable CENP-E Inhibitor.

Photoswitchable compounds are potent tools for elucidating molecular functions in dynamic cellular processes. Photoswitchable inhibitors targeting various mitotic spindle factors have been developed. In this chapter, we describe experimental methods for photo-controlling mitotic chromosome dynamics using a recently developed photoswitchable inhibitor of mitotic kinesin, CENP-E. This inhibitor undergoes reversible photoisomerization to a more inhibitory trans or less inhibitory cis state by visible or UV light irradiation, respectively, enabling photoswitching of CENP-E function both in vitro and in vivo. First, we explain the procedures used to optimize the experimental condition for efficient photoswitching of CENP-E functionality in cultured cells. We then describe how to conduct de novo photo-control of mitotic chromosome motion using the inhibitor under a microscope.

Design of Near-Infrared Emissive Molecular Switches Based on Stilbene-Appended Cyclometalated Bimetallic Ru(II)-Terpyridine Complexes.

In the present study, we have synthesized and thoroughly characterized two Ru(II) dimers with compositions [(ttpy)Ru(tpvpt')Ru(ttpy)](ClO4)3 and [(ttpy)Ru(t'pvpvpt')Ru(ttpy)](ClO4)2 incorporating phenylene-vinylene-substituted terpyridine bridging ligands capable of coordinating in both an NNN- and cyclometalated NNC-fashion. The complexes display strong absorption across the entire UV-vis spectral domain and exhibit luminescence in the NIR region (820-850 nm). The N atoms in the outer coordination sphere were employed for alteration of the photoredox behaviors of the complexes via acid-base equilibria. Decoordination of the Ru-C bonds in the presence of acid, followed by recoordination in the presence of base and heat, is also possible. Additionally, the phenylene-vinylene units in the bridging ligands facilitate trans → cis and trans-trans → trans-cis isomerization under visible light irradiation. The reverse isomerization (cis → trans and trans-cis → trans-trans) is also achieved upon UV light irradiation. Thus, "on-off" and "off-on" emission switching is facilitated through a judicious choice of external stimuli like acid, base, temperature, or light of particular wavelengths. Interestingly, the rate of photoswitching is significantly faster in the presence of acid compared to that in the absence of acid. DFT and TD-DFT calculations were also conducted to clearly visualize the electronic environment around the complex backbone and also for accurate assignment of the absorption and emission bands.

Towards Bacterial Resistance via the Membrane Strategy: Enzymatic, Biophysical and Biomimetic Studies of the Lipid cis-trans Isomerase of Pseudomonas aeruginosa.

The lipid cis-trans isomerase (Cti) is a periplasmic heme-c enzyme found in several bacteria including Pseudomonas aeruginosa, a pathogen known for causing nosocomial infections. This metalloenzyme catalyzes the cis-trans isomerization of unsaturated fatty acids in order to rapidly modulate membrane fluidity in response to stresses that impede bacterial growth. As a consequence, breakthrough in the elucidation of the mechanism of this metalloenzyme might lead to new strategies to combat bacterial antibiotic resistance. We report the first comprehensive biochemical, electrochemical and spectroscopic characterization of a Cti enzyme. This has been possible by the successful purification of Cti from P. aeruginosa (Pa-Cti) in favorable yields with enzyme activity of 0.41 μmol/min/mg when tested with palmitoleic acid. Through a synergistic approach involving enzymology, site-directed mutagenesis, Raman spectroscopy, Mössbauer spectroscopy and electrochemistry, we identified the heme coordination and redox state, pinpointing Met163 as the sixth ligand of the FeII of heme-c in Pa-Cti. Significantly, the development of an innovative assay based on liposomes demonstrated for the first time that Cti catalyzes cis-trans isomerization directly using phospholipids as substrates without the need of protein partners, answering the important question about the substrate of Cti within the bacterial membrane.

Optically controlled phase change wood for energy storage and heat release

Molecular solar thermal (MOST) fuels efficiently store solar energy and release it as heat by photoisomerization-induced phase change. However, MOSTs still struggle to meet practical demands due to its slow cis-trans isomerization rate, solvent-assisted charging and low energy storage density. Herein, we develop an optically controlled phase change wood (OCPCW) through impregnating methoxyazobenzene (mAZO) into delignified basswood with light energy storage and thermal energy release. Wood, as supporting frame, accelerates the rate of cis-trans isomerization due to the dispersion of mAZO by wood pores. In addition, the per unit storage energy density of mAZO in OCPCW can reach 307.5 J·g−1, which is higher than that of pure mAZO (229 J·g−1), due to the hydrogen bonding between cellulose and mAZO. Under sunlight irradiation, the cis-OCPCM undergoes isomerization to trans-OCPCM, releasing heat and leading to a temperature increase approximately 2 °C higher than that of delignified basswood under identical conditions. Furthermore, color changing in response to phase change, the OCPCM could be designed for encrypted and decrypted information with dual imaging modes through the color change and exothermic behavior. This work paves the way for the development of phase change wood for efficient solar energy storage and release and application in encrypted information display.

PH and light-triggered shape transformation of block copolymer particles in emulsion droplets

Dual-responsive shape-transformable block copolymer (BCP) particles have arisen great attentions because of their tunable physical and chemical characteristics triggered by external stimuli. Herein, we developed a simple yet effective strategy to realize pH and light dual-triggered shape-switchable BCP particles through the co-assembly of BCPs with photo-responsive additive 4-hydroxyazobenzene (Azo-OH) within the evaporation emulsion droplets. The formation of hydrogen bonding interactions between the Azo-OH and 4-vinylpyridine (4VP) unit increases the volume fraction of P4VP domain, in turn leading to a morphological transition of the particles from onions to pupas by tuning the Azo-OH content. Subsequent light-induced trans–cis transition of the Azo unit induces the enhancement of the hydrophilicity of the P4VP domains, giving rise to internal shape transitions of the BCP particles from pupas to onions with P4VP at the outmost-layer. Furtherly, since the hydrogen bonds between Azo-OH and 4VP group are sensitive to pH, the interfacial properties of the emulsion droplets and the assembled structures are tuned through adjusting the environment pH of the aqueous solution, causing the formation of various particle shape, including pupas, raspberries, and onions. This work offers a promising method to engineer the microstructures of polymeric assemblies, which may attract more attention on the applications of the stimuli-responsive particles.

The conformational landscape of fold-switcher KaiB is tuned to the circadian rhythm timescale

How can a single protein domain encode a conformational landscape with multiple stably folded states, and how do those states interconvert? Here, we use real-time and relaxation-dispersion NMR to characterize the conformational landscape of the circadian rhythm protein KaiB from Rhodobacter sphaeroides. Unique among known natural metamorphic proteins, this KaiB variant spontaneously interconverts between two monomeric states: the "Ground" and "Fold-switched" (FS) states. KaiB in its FS state interacts with multiple binding partners, including the central KaiC protein, to regulate circadian rhythms. We find that KaiB itself takes hours to interconvert between the Ground and FS state, underscoring the ability of a single-sequence to encode the slow process needed for function. We reveal the rate-limiting step between the Ground and FS state is the cis-trans isomerization of three prolines in the fold-switching region by demonstrating interconversion acceleration by the prolyl isomerase Cyclophilin A. The interconversion proceeds through a "partially disordered" (PD) state, where the C-terminal half becomes disordered while the N-terminal half remains stably folded. We found two additional properties of KaiB's landscape. First, the Ground state experiences cold denaturation: At 4 °C, the PD state becomes the majorly populated state. Second, the Ground state exchanges with a fourth state, the "Enigma" state, on the millisecond-timescale. We combine AlphaFold2-based predictions and NMR chemical shift predictions to predict this Enigma state is a beta-strand register shift that relieves buried charged residues, and support this structure experimentally. These results provide mechanistic insight into how evolution can design a single-sequence that achieves specific timing needed for its function.