Isotope-Labeled RNA Building Blocks for NMR Structure and Dynamics Studies

RNA structural research lags behind that of proteins, preventing a robust understanding of RNA functions. NMR spectroscopy is an apt technique for probing the structures and dynamics of RNA molecules in solution at atomic resolution. Still, RNA analysis by NMR suffers from spectral overlap and line broadening, both of which worsen for larger RNAs. Incorporation of stable isotope labels into RNA has provided several solutions to these challenges. In this review, we summarize the benefits and limitations of various methods used to obtain isotope-labeled RNA building blocks and how they are used to prepare isotope-labeled RNA for NMR structure and dynamics studies.     

DNP‐Supported Solid‐State NMR Spectroscopy of Proteins Inside Mammalian Cells

Elucidating at atomic level how proteins interact and are chemically modified in cells represents a leading frontier in structural biology. We have developed a tailored solid‐state NMR spectroscopic approach that allows studying protein structure inside human cells at atomic level under high‐sensitivity dynamic nuclear polarization (DNP) conditions. We demonstrate the method using ubiquitin (Ub), which is critically involved in cellular functioning. Our results pave the way for structural studies of larger proteins or protein complexes inside human cells, which have remained elusive to in‐cell solution‐state NMR spectroscopy due to molecular size limitations.     

Solid-state NMR spectroscopy on complex biomolecules

Biomolecular applications of NMR spectroscopy are often merely associated with soluble molecules or magnetic resonance imaging. However, since the late 1970s, solid-state NMR (ssNMR) spectroscopy has demonstrated its ability to provide atomic-level insight into complex biomolecular systems ranging from lipid bilayers to complex biomaterials. In the last decade, progress in the areas of NMR spectroscopy, biophysics, and molecular biology have significantly expanded the repertoire of ssNMR spectroscopy for biomolecular studies. This Review discusses current approaches and methodological challenges, and highlights recent progress in using ssNMR spectroscopy at the interface of structural and cellular biology.     

Structural and photochemical aspect of metal-ion-binding to a photochromic chromene annulated by crown-ether moiety

Complexation between a benzopyran entity annulated with a 15-crown-5 ether unit and three metal cations, Mg²⁺, Ba²⁺, and Pb²⁺ has been investigated by UV–vis and NMR spectroscopy. The complexes composition, the stability constants and the structural arrangements have been determined. The photochemical and thermal properties of the photochromic benzopyran derivative in absence and in the presence of metals have been studied. The metal-ion-binding ability of the fused macrocyclic entity drastically modifies photochromism by decreasing the thermal stability of photomerocyanines, whereas the metal cations are partially ejected from crown-ether cavity when benzopyran is in open configuration.     

Structures behind the amyloid aggregation of α-synuclein: an NMR based approach

The misfolding of proteins into a toxic conformation is proposed to be at the molecular foundation of a number of neurodegenerative disorders including Alzheimer's and Parkinson's diseases. Evidence that α-synuclein amyloidogenesis plays a causative role in the development of Parkinson's disease is furnished by a variety of genetic, neuropathological and biochemical studies. There is a major interest in understanding the structural and toxicity features of the various species populated along the aggregation pathway of this protein. The development of multidimensional nuclear magnetic resonance (NMR) spectroscopy in liquid and solid state over the last decade has significantly increased the scope of molecules that are amenable for structural studies. The aim of this review is to provide a picture of how NMR tools were used in concert to decipher the structural and dynamic properties of the intrinsically disordered protein α-synuclein in its native, oligomeric, fibril and membrane-bound states. Understanding the structural and molecular basis behind the aggregation pathway of α-synuclein is key to advance in the design of a therapeutic strategy.     

A multi-photo responsive photochromic dithienylethene containing coumarin derivative

A complex photochromic diarylethene derivative containing photo-responsive coumarin groups was synthesized by an efficient method. The dimerization of coumarin groups and photochromism of diarylethene can be controlled respectively to produce the four corresponding states, which were verified by ¹H NMR, fluorescent, UV–vis spectroscopy and mass spectrometry. This compound gives a unique example for the controllable switch of both optical properties and chemical composition by light and chemical stimuli.     

NMR spectroscopy tools for structure-aided drug design

Biomolecular NMR spectroscopy has expanded dramatically in recent years and is now a powerful tool for the study of structure, dynamics, and interactions of biomolecules. Previous limitations with respect to molecular size are no longer a primary barrier, and systems as large as 900 kDa were recently studied. NMR spectroscopy is already well-established as an efficient method for ligand screening. A number of recently developed techniques show promise as aids in structure-based drug design, for example, in the rapid determination of global protein folds, the structural characterization of ligand-protein complexes, and the derivation of thermodynamic parameters. An advantage of the method is that all these interactions can be studied in solution--time-consuming crystallization is not necessary. This Review focuses on recent developments in NMR spectroscopy and how they might be of value in removing some of the current "bottlenecks" in structure-based drug discovery.     

氧化还原对Lindqvist型多金属氧簇复合物自组装的动态调控

Dynamic regulation of self-assembly is of vital importance in chemistry, biology and material science thanks to its great potential for development of smart materials and devices. Polyoxometalates (POMs) are a class of functional inorganic nanoclusters, which has become one of the excellent building blocks for supramolecular self-assemblies, especially when covalently or non-covalently modified by organic species. As typical stimuli-responsive functional clusters, the POMs could be photochemically or electrochemically reduced to mixed-valence states, of which the structural integrity remains even after encountering stepwise multi-electron redox process. The intriguing photochromism of the POMs in different states exhibits distinct photophysical properties, which motivates us to exploit the dynamic self-assemblies of POM-based complexes. The divalent Lindqvist-type hexamolybdate cluster [Mo₆O₁₉]^2- is one of the least negative-charged POMs, which is the ideal building blocks to construct novel assembly structures. Based on this motivation, herein, a single chain surfactant-encapsulated polyoxometalate (POM) complex (ODTA)₂[Mo₆O₁₉] was prepared by simple counterion replacement of Lindqvist-type (TBA)₂[Mo₆O₁₉] with octadecyltrimethylammonium (ODTA) in acetonitrile solution. The structure of the POM complex was confirmed by ¹H nuclear magnetic resonance (NMR), Fourier transform infrared (FT-IR) spectroscopy, thermogravimetric analysis (TGA) and elemental analysis. The solution of complex (ODTA)₂[Mo₆O₁₉] in the mixed solvents of acetonitrile and isopropanol with the volume ration of 4 to 1 exhibited reversible photochromism upon alternate UV light irradiation and air exposure. Upon UV light irradiation, the light yellow transparent solution of (ODTA)₂[Mo₆O₁₉] turned into blue quickly. The new broad absorption band appearing at ca.751 nm assigned to the Mo^V → Mo^VI intervalence charge-transfer (IVCT) transition, indicated the formation of reduced POM, as revealed by UV-Vis absorption spectra. After exposed to air, the blue solution was bleached. The alternate photochromism could be conducted for multiple cycles. Helical self-assembled morphology of (ODTA)₂[Mo₆O₁₉] was formed in acetonitrile/isopropanol, characterized by scanning electron microscope (SEM), transmission electron microscopy (TEM) and X-ray diffraction (XRD) methods. More interestingly, morphology transformation of the complex from helical strips to spherical assemblies occurred accompanied by photochromism occurrence. The morphology evolution during the photochromism process experienced from shortened helical strips through sea urchin-like aggregates to spherical assemblies. Most significantly, the helical assemblies could be recovered again after air oxidation, implying the reversible morphology transformation driven by redox stimulus. The redox-modulated reversible self-assembly is driven by the variation of electrostatic attraction between organic cations and inorganic anions as well as the electrostatic repulsion between inorganic ionic clusters, proved by X-ray photoelectron spectroscopy (XPS) and ¹H NMR spectra. The results will contribute to better understanding the mechanism of dynamic assemblies and inspire the precise fabrication of advanced smart materials.     

Phytochrome,the Visual Pigment of Plants

Plants require light for photosynthesis. In order to adapt to the light conditions in their particular habitat, they have developed various photoreceptor systems. Of these, phytochrome allows even two-color vision in the red/far-red region. The photoreceptor phytochrome is of interest not only to botanists, but also to natural product chemists, photochemists, biochemists, photobiologists, and recently molecular biologists. Despite numerous studies, there are still considerable gaps in our knowledge of this photoreceptor. This article first describes the basic structural studies of the tetrapyrrole chromophore and its photochemical cis–trans isomerization, which is the source of the chromoprotein's photochromism. In the section on the protein moiety, beside other topics, the domain structure of phytochrome and the conformational changes during phototransformation are discussed. Finally, the known phytochrome genes are used to derive phylogenetic relationships, and possible structure–function relationships are discussed.     

Studies on solid-state proton transfer along hydrogen bond of pyrazolone-ring

Evidence from the time-dependent UV-vis reflection spectra studies indicates the compound 1-phenyl-3-methyl-4-(4-methylbenzal)-5-pyrazolone 4-ethylthiosemicarbazone (PM4MBP-ETSC) undergoes a solid-state photochromism. The reaction rate constant was studied by the first-order kinetics curves. X-ray single crystal structural analysis shows that the pyrazolone-ring stabilizes in the keto form. The conclusion can be made that its photochromism in crystalline is associated with a photoinduced proton transfer reaction (inter- and intra-molecular hydrogen transfer) along hydrogen bond leading to a colored tautomer as the compound crystallizes in H-bonded supramolecular configuration.     

Synthesis and photochromism of dimers of 4,5- diaryl-2-(2,5-dimethylthiophen-3-yl)imidazolyl

4,5-Diphenyl, 4,5-di(4-methylphenyl), 4,5-di(4-methoxyphenyl)-2-(2,5-dimethylthioph-en-3-yl)imidazoles were synthesized. Oxidation of the obtained imidazoles with potassium ferricyanide in water-alcohol solution of alkali gave the corresponding dimers. The structures were characterized by IR, 1H NMR, mass spectroscopy and elemental analysis. The dimers showed photochromism in solution on irradiation.     

3-甲基-1,4-二苯氧基-9,10-蒽醌的合成及其光致变色性

合成了3-甲基-1,4-二苯氧基-9,10-蒽醌,其结构经1^H NMR,13^C NMR,IR和MS表征,并通过紫外光谱探讨了其光致变色性,讨论了取代基对蒽醌类化合物光致变色性的影响。     

Unwinding of the C‐Terminal Residues of Neuropeptide Y is critical for Y2 Receptor Binding and Activation

Despite recent breakthroughs in the structural characterization of G‐protein‐coupled receptors (GPCRs), there is only sparse data on how GPCRs recognize larger peptide ligands. NMR spectroscopy, molecular modeling, and double‐cycle mutagenesis studies were integrated to obtain a structural model of the peptide hormone neuropeptide Y (NPY) bound to its human G‐protein‐coupled Y₂ receptor (Y₂R). Solid‐state NMR measurements of specific isotope‐labeled NPY in complex with in vitro folded Y₂R reconstituted into phospholipid bicelles provided the bioactive structure of the peptide. Guided by solution NMR experiments, it could be shown that the ligand is tethered to the second extracellular loop by hydrophobic contacts. The C‐terminal α‐helix of NPY, which is formed in a membrane environment in the absence of the receptor, is unwound starting at T³² to provide optimal contacts in a deep binding pocket within the transmembrane bundle of the Y₂R.     

Structural characterization of chromone C-glucosides in a toxic herbal remedy

Two novel compounds, 8-C-D-glucopyranosyl-7-hydroxy-5-methylchromone-2-carboxylic acid and a 2-O'-p-coumaroyl derivative thereof, were identified in a herbal tea that caused severe vomiting in a South African patient who had taken the traditional remedy to clean his stomach. For structural characterization, electrospray (ES) ionization in combination with collision-induced dissociation (CID) and tandem mass spectrometry (MS/MS) were used, as well as UV and nuclear magnetic resonance (NMR) spectroscopy. Specific ions or neutral losses generated under conditions of ES-MS/CID/MS permitted the establishment of structural features such as the free carboxyl group, the C-hexosidic part and the p-coumaroyl group. NMR spectroscopy was necessary to support the structure of the chromone-type aglycone and the glucosidic parts. Since the compounds are structurally related to aloesin and aloeresin A, which are chemotaxonomic markers of Aloe species, and have not been previously reported, we propose that they were formed by oxidative degradation during preparation of the herbal tea from an Aloe species or during its storage.     

The structure of phosphate and borosilicate glasses and their structural evolution at high temperatures as studied with solid state NMR spectroscopy: Phase separation,crystallisation and dynamic species exchange

In this contribution we present an in-depth study of the network structure of different phosphate based and borosilicate glasses and its evolution at high temperatures. Employing a range of advanced solid state NMR methodologies, complemented by the results of XPS, the structural motifs on short and intermediate length scales are identified. For the phosphate based glasses, at temperatures above the glass transition temperature T_g, structural relaxation processes and the devitrification of the glasses were monitored in situ employing MAS NMR spectroscopy and X-ray diffraction. Dynamic species exchange involving rapid P–O–P and P–O–Al bond breaking and reforming was observed employing in situ ²⁷Al and ³¹P MAS NMR spectroscopy and could be linked to viscous flow. For the borosilicate glasses, an atomic scale investigation of the phase separation processes was possible in a combined effort of ex situ NMR studies on glass samples with different thermal histories and in situ NMR studies using high temperature MAS NMR spectroscopy including ¹¹B MAS, ²⁹Si MAS and in situ ²⁹Si{¹¹B} REAPDOR NMR spectroscopy.     

Solid-state photochromism of chromenes: enhanced photocoloration and observation of unstable colored species at low temperatures

Solid-state photochromism of benzopyrans and naphthopyrans (chromenes) was investigated in the temperature range between 300 and 80 K. Variable-temperature diffuse reflectance spectroscopy of microcrystalline powders showed that the extent of photocoloration was greatly enhanced at low temperatures. All the chromenes examined exhibited solid-state photochromism at low temperatures, even when they showed little or no photocoloration at room temperature. The solid-state photochromic properties of the chromenes were quite similar to those reported for analogous photochromic compounds of spiropyrans and spirooxazines, which indicates that these classes of compounds are generally photochromic even in the solid state. Photobleaching reactions of the colored merocyanine forms proceeded at low temperatures through the formation of a colorless intermediate, instead of directly resuming the original closed form. In addition to two stable planar merocyanine forms, which are usually observed in the photochromic reactions in solution, photoreactions at low temperatures allowed us to observe unstable colored species, which were tentatively assigned as nonplanar cisoid forms, and were stabilized in the solid state at low temperatures.     

Reconstitution of the Cytb5–CytP450 Complex in Nanodiscs for Structural Studies using NMR Spectroscopy

Cytochrome P450s (P450s) are a superfamily of enzymes responsible for the catalysis of a wide range of substrates. Dynamic interactions between full‐length membrane‐bound P450 and its redox partner cytochrome b₅ (cytb₅) have been found to be important for the enzymatic activity of P450. However, the stability of the circa 70 kDa membrane‐bound complex in model membranes renders high‐resolution structural NMR studies particularly difficult. To overcome these challenges, reconstitution of the P450–cytb₅ complex in peptide‐based nanodiscs, containing no detergents, has been demonstrated, which are characterized by size exclusion chromatography and NMR spectroscopy. In addition, NMR experiments are used to identify the binding interface of the P450–cytb₅ complex in the nanodisc. This is the first successful demonstration of a protein–protein complex in a nanodisc using NMR structural studies and should be useful to obtain valuable structural information on membrane‐bound protein complexes.     

Photochromism of organometallic compounds with structural rearrangement

This article introduces photochromic properties together with structures of organometallic compounds that undergo photo-induced structural rearrangement. The aim of this review is to survey the research on photochromism by using organometallics which possess by their own nature the properties responsible for the photochromism such as bonding and structural fluxionality, electronic state fluctuation, and photochemically active characteristic in both solution and the solid state. Therefore, the organometallics which include the well-characterized organic photochromic moieties, considered to be derivatives of such kinds of organic photochromic compounds, are excluded in this article. Mono-, di-, and poly-nuclear organometallic compounds are presented based on the reaction types such as linkage isomerization, haptotropic rearrangement, and reorganization of metal–ligand and/or metal–metal bonds. Very recently, the crystalline-state photochromism is becoming an attractive field of photochromic chemistry. As a demonstrative example, the photochromism of organometallic rhodium dinuclear complexes having a dithionite ligand (μ-O₂SSO₂), which shows 100% reversible interconversion in the crystalline-state and have been developed in the authors’ laboratory, will be discussed.     

Synthesis and properties of template-promoted switchable dithienylethenebased macrocycles

Three switchable macrocycles based on photochromic dithienylethene were synthesized under the template of dibenzylammonium hexafluorophosphate. Their structure were well-confirmed by NMR, ESI-MS and X-ray diffraction. Their photochromism indicated that they showed good reversibility in solution. Additionally, the theoretical calculation suggested that photoirradiation can change the cavity of macrocycles.     

The NMR added value to the green foodomics perspective: Advances by machine learning to the holistic view on food and nutrition

Food is a complex matter, literally. From production to functionalization, from nutritional quality engineering to predicting effects on health, the interest in finding an efficient physicochemical characterization of food has boomed in recent years. The sheer complexity of characterizing food and its interaction with the human organism has however made the use of data driven approaches in modeling a necessity. High-throughput techniques, such as nuclear magnetic resonance (NMR) spectroscopy, are well suited for omics data production and, coupled with machine learning, are paving a promising way of modeling food–human interaction. The foodomics approach sets the framework for omic data integration in food studies, in which NMR experiments play a key role. NMR data can be used to assess nutritional qualities of food, helping the design of functional and sustainable sources of nutrients; detect biomarkers of intake and study how they impact the metabolism of different individuals; study the kinetics of compounds in foods or their by-products to detect pathological conditions; and improve the efficiency of in silico models of the metabolic network.