In Situ Imaging of Virus-Infected Cells by Cryo-Electron Tomography: An Overview.

Cryo-electron tomography (cryo-ET) has emerged as a powerful tool in structural biology to study viruses and is undergoing a resolution revolution. Enveloped viruses comprise several RNA and DNA pleomorphic viruses that are pathogens of clinical importance to humans and animals. Considerable efforts in cryogenic correlative light and electron microscopy (cryo-CLEM), cryogenic focused ion beam milling (cryo-FIB), and integrative structural techniques are helping to identify virus structures within cells leading to a rise of in situ discoveries shedding light on how viruses interact with their hosts during different stages of infection. This chapter reviews recent advances in the application of cryo-ET in imaging enveloped viruses and the structural and mechanistic insights revealed studying the viral infection cycle within their eukaryotic cellular hosts, with particular attention to viral entry, replication, assembly, and egress during infection.

Structural Characterization and Cytotoxic Activity Evaluation of Ulvan Polysaccharides Extracted from the Green Algae Ulva papenfussii.

Ulvan, a sulfated heteropolysaccharide with structural and functional properties of interest for various uses, was extracted from the green seaweed Ulva papenfussii. U. papenfussii is an unexplored Ulva species found in the South China Sea along the central coast of Vietnam. Based on dry weight, the ulvan yield was ~15% (w/w) and the ulvan had a sulfate content of 13.4 wt%. The compositional constitution encompassed L-Rhamnose (Rhap), D-Xylose (Xylp), D-Glucuronic acid (GlcAp), L-Iduronic acid (IdoAp), D-Galactose (Galp), and D-Glucose (Glcp) with a molar ratio of 1:0.19:0.35:0.52:0.05:0.11, respectively. The structure of ulvan was determined using High-Performance Liquid Chromatography (HPLC), Fourier Transform Infrared Spectroscopy (FT-IR), and Nuclear Magnetic Resonance spectroscopy (NMR) methods. The results showed that the extracted ulvan comprised a mixture of two different structural forms, namely ("A3s") with the repeating disaccharide [→4)-ß-D-GlcAp-(1→4)-α-L-Rhap 3S-(1→]n, and ("B3s") with the repeating disaccharide [→4)-α-L-IdoAp-(1→4)-α-L-Rhap 3S(1→]n. The relative abundance of A3s, and B3s was 1:1.5, respectively. The potential anticarcinogenic attributes of ulvan were evaluated against a trilogy of human cancer cell lineages. Concomitantly, Quantitative Structure-Activity Relationship (QSAR) modeling was also conducted to predict potential adverse reactions stemming from pharmacological interactions. The ulvan showed significant antitumor growth activity against hepatocellular carcinoma (IC50 ≈ 90 µg/mL), human breast cancer cells (IC50 ≈ 85 µg/mL), and cervical cancer cells (IC50 ≈ 67 µg/mL). The QSAR models demonstrated acceptable predictive power, and seven toxicity indications confirmed the safety of ulvan, warranting its candidacy for further in vivo testing and applications as a biologically active pharmaceutical source for human disease treatment.

N-Heterocyclic Carbene Copper (I) Complexes Incorporating Pyrene Chromophore: Synthesis, Crystal Structure, and Luminescent Properties.

Luminescent N-heterocyclic carbene chloride copper (I) complexes incorporating pyrene chromophore (1-Pyrenyl-NHC-R)-Cu-Cl, (3, 4) have been prepared and fully characterized. Two complexes were prepared with R = methyl (3) and R = naphthyl groups (4) at the nitrogen center of the carbene unit to tune their electronic properties. The molecular structures of 3 and 4 have been elucidated by X-ray diffraction and confirm the formation of the target compounds. Preliminary results reveal that all compounds including the imidazole-pyrenyl ligand 1 are emissive in the blue region at room temperature in solution and in solid-state. All complexes display quantum yields comparable or higher when compared to the parent pyrene molecule. Interestingly replacement of the methyl by naphthyl group increases the quantum yield by almost two-folds. These compounds might show promise for applications as optical displays.

Anti-phytopathogenic-bacterial fatty acids from the mycelia of the edible mushroom Agaricus blazei.

Five compounds including a new compound (1) were isolated from mycelia of a mushroom-forming fungus Agaricus blazei. Compound 2 was isolated from nature for the first time. Their structures were determined by the interpretation of spectroscopic data. In the bioassay examining growth inhibitory activity against phytopathogenic bacteria Clavibacter michiganensis, Burkholderia glumae, and Peptobacterium carotovorum, all the compounds showed inhibition effects on C. michiganensis. Compounds 3 and 4 also showed weak inhibitory activity against growth of B. glumae.

A new lanostane triterpenoid from the mushroom Hypholoma fasciculare.

A novel compound (1) and 3 known compounds (2-4) were isolated from the fruiting bodies of Hypholoma fasciculare. The structure of 1 was determined by the interpretation of spectroscopic data. Compounds 2-4 were identified by comparing the spectra data of known compounds. In the bioassay examining growth inhibitory activity against phytopathogenic bacteria Clavibacter michiganensis, Burkholderia glumae, and Peptobacterium carotovorum, compounds 1, 2, and 4 showed inhibition effects on C. michiganensis only.

Actinoflavosides B-D, Flavonoid Type Glycosides from Tidal Mudflat-Derived Actinomyces.

Three new secondary metabolites, actinoflavosides B-D (1-3), were discovered in the culture broth of two actinomycete strains (JML48 and JMS33) that were isolated from tidal mudflat sediment in Muan, Republic of Korea. The planar structures of the actinoflavosides were elucidated by MS, UV, and NMR analyses. The stereochemistry of an aminosugar, 2,3,6-trideoxy-3-amino-ribopyranoside in the actinoflavosides was determined by J-based configuration analysis using values obtained from DQF-COSY experiments and modified Mosher's method. Actinoflavosides B-D (1-3) displayed antibacterial activity against Pseudomonas aeruginosa, and actinoflavoside D (3) significantly increased IL-2 production in mouse splenocytes.

Insights into Cytotoxic Behavior of Lepadins and Structure Elucidation of the New Alkaloid Lepadin L from the Mediterranean Ascidian Clavelina lepadiformis.

The chemical investigation of the Mediterranean ascidian Clavelina lepadiformis has led to the isolation of a new lepadin, named lepadin L, and two known metabolites belonging to the same family, lepadins A and B. The planar structure and relative configuration of the decahydroquinoline ring of lepadin L were established both by means of HR-ESIMS and by a detailed as extensive analysis of 1D and 2D NMR spectra. Moreover, microscale derivatization of the new alkaloid lepadin L was performed to assess the relative configuration of the functionalized alkyl side chain. Lepadins A, B, and L were tested for their cytotoxic activity on a panel of cancer cell lines (human melanoma [A375], human breast [MDA-MB-468], human colon adenocarcinoma [HT29], human colorectal carcinoma [HCT116], and mouse myoblast [C2C12]). Interestingly, a deeper investigation into the mechanism of action of the most cytotoxic metabolite, lepadin A, on the A375 cells has highlighted its ability to induce a strongly inhibition of cell migration, G2/M phase cell cycle arrest and a dose-dependent decrease of cell clonogenity, suggesting that it is able to impair self-renewing capacity of A375 cells.

Rational Design of Mono- and Bi-Nuclear Cyclometalated Ir(III) Complexes Containing Di-Pyridylamine Motifs: Synthesis, Structure, and Luminescent Properties.

Heteroleptic cyclometalated iridium (III) complexes (1-3) containing di-pyridylamine motifs were prepared in a stepwise fashion. The presence of the di-pyridylamine ligands tunes their electronic and optical properties, generating blue phosphorescent emitters at room temperature. Herein we describe the synthesis of the mononuclear iridium complexes [Ir(ppy)2(DPA)][OTf] (1), (ppy = phenylpyridine; DPA = Dipyridylamine) and [Ir(ppy)2(DPA-PhI)][OTf] (2), (DPA-PhI = Dipyridylamino-phenyliodide). Moreover, the dinuclear iridium complex [Ir(ppy)2(L)Ir(ppy)2][OTf]2 (3) containing a rigid angular ligand "L = 3,5-bis[4-(2,2'-dipyridylamino)phenylacetylenyl]toluene" and displaying two di-pyridylamino groups was also prepared. For comparison purposes, the related dinuclear rhodium complex [Rh (ppy)2(L)Rh(ppy)2][OTf]2 (4) was also synthesized. The x-ray molecular structure of complex 2 was reported and confirmed the formation of the target molecule. The rhodium complex 4 was found to be emissive only at low temperature; in contrast, all iridium complexes 1-3 were found to be phosphorescent in solution at 77 K and room temperature, displaying blue emissions in the range of 478-481 nm.

Identification of Cyclic Dipeptides and a New Compound (6-(5-Hydroxy-6-methylheptyl)-5,6-dihydro-2H-pyran-2-one) Produced by Streptomyces fungicidicus against Alternaria solani.

As an important microbial resource, Actinomycetes, especially Streptomyces, have important application values in medicine and biotechnology. Streptomyces fungicidicus SYH3 was isolated from soil samples in tomato-growing areas and showed good inhibitory effects on Alternaria solani in tomato. To obtain pure active compounds, SYH3 fermentation broth was subjected to XAD-16 macroporous resin and silica gel column chromatography. Combined with the repeated preparation and separation of preparative high-performance liquid chromatography (HPLC), a total of four monomer compounds were obtained after activity tracking. Compound 4 was identified as a new six-membered lactone ring compound named 6-(5-hydroxy-6-methylheptyl)-5,6-dihydro-2H-pyran-2-one by 1D and 2D nuclear magnetic resonance (NMR) data and mass spectrometry (MS). The other three active compounds belong to the cyclodipeptide, and their half maximal inhibitory concentration (IC50) values against A. solani were 43.4, 42.9, and 30.6 µg/mL, respectively. Compound 4 significantly inhibited the spore germination and induced swollen and deformed local hyphae of A. solani with an IC50 value of 24.9 µg/mL. Compound 4 also had broad-spectrum antifungal activity and had a good antifungal effect on the tested plant-pathogenic fungi. The modes of action of new compound (4) still require further investigation, representing a novel and effective anti-fungal agent for future application.

Highly Sensitive Determination of Amino Acids by LC-MS under Neutral Conditions.

Peptide drug leads possess unusual structural features that allow them to exert their unique biological activities and ideal physicochemical properties. In particular, these peptides often have D-amino acids, and therefore the absolute configurations of the component amino acids have to be elucidated during the structural determination of newly isolated peptide drug leads. Recently, we developed the highly sensitive labeling reagents D/L-FDVDA and D/L-FDLDA for the structural determination of the component amino acids in peptides. In an LC-MS-based structural study of peptides, these reagents enabled us to detect infinitesimal amounts of amino acids derived from mild degradative analysis of the samples. Herein, we firstly report the improved LC-MS protocols for the highly sensitive analyses of amino acids. Second, two new labeling reagents were synthesized and their detection sensitivities evaluated. These studies increase our understanding of the structural basis of these highly sensitive labeling reagents, and should provide opportunities for future on-demand structural modifications of the reagents to enhance their hydrophobicity, stability, and affinity for applications to specialized HPLC columns.

Hydrogen Delocalization in an Asymmetric Biomolecule: The Curious Case of Alpha-Fenchol.

Rotational microwave jet spectroscopy studies of the monoterpenol α-fenchol have so far failed to identify its second most stable torsional conformer, despite computational predictions that it is only very slightly higher in energy than the global minimum. Vibrational FTIR and Raman jet spectroscopy investigations reveal unusually complex OH and OD stretching spectra compared to other alcohols. Via modeling of the torsional states, observed spectral splittings are explained by delocalization of the hydroxy hydrogen atom through quantum tunneling between the two non-equivalent but accidentally near-degenerate conformers separated by a low and narrow barrier. The energy differences between the torsional states are determined to be only 16(1) and 7(1) cm-1hc for the protiated and deuterated alcohol, respectively, which further shrink to 9(1) and 3(1) cm-1hc upon OH or OD stretch excitation. Comparisons are made with the more strongly asymmetric monoterpenols borneol and isopinocampheol as well as with the symmetric, rapidly tunneling propargyl alcohol. In addition, the third-in contrast localized-torsional conformer and the most stable dimer are assigned for α-fenchol, as well as the two most stable dimers for propargyl alcohol.

Structural and DNA binding properties of mycobacterial integration host factor mIHF.

In bacteria, nucleoid associated proteins (NAPs) take part in active chromosome organization by supercoil management, three-dimensional DNA looping and direct transcriptional control. Mycobacterial integration host factor (mIHF, rv1388) is a NAP restricted to Actinobacteria and essential for survival of the human pathogen Mycobacterium tuberculosis. We show in vitro that DNA binding by mIHF strongly stabilizes the protein and increases its melting temperature. The structure obtained by Nuclear Magnetic Resonance (NMR) spectroscopy characterizes mIHF as a globular protein with a protruding alpha helix and a disordered N-terminus, similar to Streptomyces coelicolor IHF (sIHF). NMR revealed no residues of high flexibility, suggesting that mIHF is a rigid protein overall that does not undergo structural rearrangements. We show that mIHF only binds to double stranded DNA in solution, through two DNA binding sites (DBSs) similar to those identified in the X-ray structure of sIHF. According to Atomic Force Microscopy, mIHF is able to introduce left-handed loops of ca. 100 nm size (~300 bp) in supercoiled cosmids, thereby unwinding and relaxing the DNA.

The Scent of Maibowle - π Electron Localization in Coumarin from Its Microwave-Determined Structure.

The microwave spectra of the natural substance coumarin, a planar aromatic molecule with the specific scent of maibowle, a popular fruit punch served in spring and early summer, were recorded using a molecular jet Fourier transform microwave spectrometer working in the frequency range from 4.0 to 26.5 GHz. The rotational constants and centrifugal distortion constants were determined with high precision, reproducing the spectra to experimental accuracy. The spectra of all singly-substituted 13 C and 18 O isotopologues were observed in their natural abundances to determine the experimental heavy atom substitution rs and semi-experimental equilibrium reSE structures. The experimental bond lengths and bond angles were compared to those obtained from quantum chemical calculations and those of related molecules reported in the literature with benzene as the prototype. The alternation of the C-C bond lengths to the value of 1.39 Šfound for benzene reflects the localization of π electrons in coumarin, where the benzene ring and the lactone-like chain -CH=CH-(C=O)-O- are fused. The large, negative inertial defect of coumarin is consistent with out-of-plane vibrations of the fused rings.

Structural Changes Induced by Quinones: High-Resolution Microwave Study of 1,4-Naphthoquinone.

1,4-Naphthoquinone (1,4-NQ) is an important product of naphthalene oxidation, and it appears as a motif in many biologically active compounds. We have investigated the structure of 1,4-NQ using chirped-pulse Fourier transform microwave spectroscopy and quantum chemistry calculations. The rotational spectra of the parent species, and its 13 C and 18 O isotopologues were observed in natural abundance, and their spectroscopic parameters were obtained. This allowed the determination of the substitution rs , mass-weighted rm and semi-experimental reSE structures of 1,4-NQ. The obtained structural parameters show that the quinone moiety mainly changes the structure of the benzene ring where it is inserted, modifying the C-C bonds to having predominantly single or double bond character. Furthermore, the molecular electrostatic surface potential reveals that the quinone ring becomes electron deficient while the benzene ring remains a nucleophile. The most electrophilic areas are the hydrogens attached to the double bond in the quinone ring. Knowledge of the nucleophilic and electrophilic areas in 1,4-NQ will help understanding its behaviour interacting with other molecules and guide modifications to tune its properties.

Role of integrative structural biology in understanding transcriptional initiation.

Integrative structural biology combines data from multiple experimental techniques to generate complete structural models for the biological system of interest. Most commonly cross-linking data sets are employed alongside electron microscopy maps, crystallographic structures, and other data by computational methods that integrate all known information and produce structural models at a level of resolution that is appropriate to the input data. The precision of these modelled solutions is limited by the sparseness of cross-links observed, the length of the cross-linking reagent, the ambiguity arisen from the presence of multiple copies of the same protein, and structural and compositional heterogeneity. In recent years integrative structural biology approaches have been successfully applied to a range of RNA polymerase II complexes. Here we will provide a general background to integrative structural biology, a description of how it should be practically implemented and how it has furthered our understanding of the biology of large transcriptional assemblies. Finally, in the context of recent breakthroughs in microscope and direct electron detector technology, where increasingly EM is capable of resolving structural features directly without the aid of other structural techniques, we will discuss the future role of integrative structural techniques.

Structural determination and in vitro tumor cytotoxicity evaluation of five new cycloartane glycosides from Asplenium ruprechtii Sa. Kurata.

Five new cycloartane glycosides, named aspleniumside A - E, were discovered and characterized by re-investigated the remaining extracts of the whole plant of Asplenium ruprechtii Sa. Kurata, a famous folk medicine for treating thromboangitis obliterans in China, Japan, and Korea. Compounds 3-5 possessed the 9,19-seco-cycloartane-9,11-en triterpene aglycone with 3,7(or 23),24,25,30-highly oxidized methylene, methylene or quaternary carbons, that was found in this species for the first time. The stereo-chemistry of all new compounds were fully discussed by extensive analysis of the 1D and 2D NMR data, and comparisons with those data of known compounds. 24R configuration was determined here which indicated the different growing areas of the same species could influence the secondary metabolic behavior, leading to the differences in chemical composition. All glycoside groups were determined as ß-d-glucopyranosyl by 1H coupling constant of anomeric protons and co-TLC of the acid hydrolysate with d-glucose. All the cycloartane glycosides were evaluated against HL-60 and HepG2 cells for cytotoxicity, compounds 1-3, showed potential cytotoxicity with the IC50 in range of 18-60 µM, while the standard sorafenib showed IC50 value of 10.61 ± 0.43 and 13.43 ± 1.12 µM against HL-60 and HepG2, respectively. The results attained in this study indicated that cycloartane glycosides should be the cytotoxicity substance in A. ruprechtii Sa. Kurata, and had the potential to be developed as tumor cytotoxicity agent applied in clinic.

Practical aspects of oligopeptide AAKLVFF as an alignment medium for the measurements of residual dipolar coupling of organic molecules.

Practical aspects of the oligopeptide AAKLVFF as an alignment medium are discussed, including large-scale synthesis of the oligopeptide, detailed description of preparation of the alignment medium, and acquisition of the RDCs. The resulting orienting medium is stable and highly homogeneous with tunable alignment strength in methanol.

Structural Determination of a New Cycloartane Glycoside from Asplenium ruprechtii.

We characterized a new cycloartane glycoside, herein known as aspleniumside F (1), along with five known compounds as kaempferol-3-O-[(6-O-(E)-feruloyl)-ß-D-glucopyranosyl]-(1→2)-ß-D-galacopyranoside (2), quercetin-3-O-[(6-O-(E)-feruloyl)-ß-D-glucopyranosyl]-(1→2)-ß-D-glucopyranoside (3), kaempferol-3-O-[(6-O-(E)-caffeoyl)-ß-D-glucopyranosyl]-(1→2)-ß-D-glucopyranoside (4), kaempferol-3-O-[(6-O-(E)-caffeoyl)-ß-D-glucopyranosyl]-(1→2)-ß-D-glucopyranosyl-7-O-ß-D-glucopyranoside (5), and kaempferol-3-O-[(6-O-p-coumaroyl)-ß-D-glucopyranosyl]-(1→2)-ß-D-glucopyranosyl-7-O-ß-D-glucopyranoside (6), from Asplenium ruprechtii Sa. Kurata, a folk medicine widely used to treat Thromboangiitis obliterans in China, Japan, and Korea. Based on spectroscopic, mainly 1D-, 2D-NMR and (+)-HR-ESI-MS, analyses as well as through comparisons with previous reports, its chemical structure was determined as 3ß,24,30-tri-ß-D-glucopyranosyl-23,25-dihydroxycycloartane (= (23R,24R)-3ß,24-bis-(ß-D-glucopyranosyloxy)-23,25-dihydroxy-9ß-9,19-cyclolanostan-29-yl ß-D-glucopyranoside). According to the 1 H coupling constant of anomeric protons and co-TLC of the acid hydrolysate with D-glucose, all three glycoside groups in 1 were revealed as ß-D-glucopyranosyl. Furthermore, SOD-like antioxidant activity evaluation via IC50 of 12.43, 6.78, 9.12, 6.94 and 4.85 µM revealed that compounds 2-6 had bioactivity.

In Situ Electron Diffraction Tomography Using a Liquid-Electrochemical Transmission Electron Microscopy Cell for Crystal Structure Determination of Cathode Materials for Li-Ion batteries.

We demonstrate that changes in the unit cell structure of lithium battery cathode materials during electrochemical cycling in liquid electrolyte can be determined for particles of just a few hundred nanometers in size using in situ transmission electron microscopy (TEM). The atomic coordinates, site occupancies (including lithium occupancy), and cell parameters of the materials can all be reliably quantified. This was achieved using electron diffraction tomography (EDT) in a sealed electrochemical cell with conventional liquid electrolyte (LP30) and LiFePO4 crystals, which have a well-documented charged structure to use as reference. In situ EDT in a liquid environment cell provides a viable alternative to in situ X-ray and neutron diffraction experiments due to the more local character of TEM, allowing for single crystal diffraction data to be obtained from multiphased powder samples and from submicrometer- to nanometer-sized particles. EDT is the first in situ TEM technique to provide information at the unit cell level in the liquid environment of a commercial TEM electrochemical cell. Its application to a wide range of electrochemical experiments in liquid environment cells and diverse types of crystalline materials can be envisaged.

Structural Determination of Lysosphingomyelin-509 and Discovery of Novel Class Lipids from Patients with Niemann-Pick Disease Type C.

Niemann-Pick disease type C (NPC) is an autosomal recessive disorder caused by the mutation of cholesterol-transporting proteins. In addition, early treatment is important for good prognosis of this disease because of the progressive neurodegeneration. However, the diagnosis of this disease is difficult due to a variety of clinical spectrum. Lysosphingomyelin-509, which is one of the most useful biomarkers for NPC, was applied for the rapid and easy detection of NPC. The fact that its chemical structure was unknown until recently implicates the unrevealed pathophysiology and molecular mechanisms of NPC. In this study, we aimed to elucidate the structure of lysosphingomyelin-509 by various mass spectrometric techniques. As our identification strategy, we adopted analytical and organic chemistry approaches to the serum of patients with NPC. Chemical derivatization and hydrogen abstraction dissociation-tandem mass spectrometry were used for the determination of function groups and partial structure, respectively. As a result, we revealed the exact structure of lysosphingomyelin-509 as N-acylated and O-phosphocholine adducted serine. Additionally, we found that a group of metabolites with N-acyl groups were increased considerably in the serum/plasma of patients with NPC as compared to that of other groups using targeted lipidomics analysis. Our techniques were useful for the identification of lysosphingomyelin-509.