Synthetic biomolecular condensates to engineer eukaryotic cells

The compartmentalization of specific functions into specialized organelles is a key feature of eukaryotic life. In particular, dynamic biomolecular condensates that are not membrane enclosed offer exciting opportunities for synthetic biology. In recent years, multiple approaches to generate and control condensates have been reported. Notably, multiple orthogonally translating organelles were designed that enable precise protein engineering inside living cells. Despite being built from only very few components, orthogonal translation can be engineered with subresolution precision at different places inside the same cell to create mammalian cells with multiple expanded genetic codes. This provides a pathway to engineer multiple proteins with multiple and distinct functionalities inside living eukaryotes and provides a general strategy toward spatially orthogonal enzyme engineering.     

Towards a science of informed matter

Over the last couple of decades, a call has begun to resound in a number of distinct fields of inquiry for a reattachment of form to matter, for an understanding of 'information' as inherently embodied, or, as Jean-Marie Lehn calls it, for a "science of informed matter." We hear this call most clearly in chemistry, in cognitive science, in molecular computation, and in robotics-all fields looking to biological processes to ground a new epistemology. The departure from the values of a more traditional epistemological culture can be seen most clearly in changing representations of biological development. Where for many years now, biological discourse has accepted a sharp distinction (borrowed directly from classical computer science) between information and matter, software and hardware, data and program, encoding and enactment, a new discourse has now begun to emerge in which these distinctions have little meaning. Perhaps ironically, much of this shift depends on drawing inspiration from just those biological processes which the discourse of disembodied information was intended to describe.     

Water dimers connect [Cu(cda)(py)3] (cda = pyridine-4-hydroxy-2,6-dicarboxylate, py = pyridine) complex units to left- and right-handed helices that form a tubular coordination polymer through supramolecular bonding

The reaction between pyridine-4-hydroxy-2,6-dicarboxylic acid (cdaH₂) and Cu(NO₃)₂ · 3H₂O afford products that depend on the reaction conditions applied. In presence of excess of aqueous pyridine (1:2 v/v), equimolar amounts of the reactants form {[Cu(cda)(py)₃]₂ · 5H₂O}_n (1). In this complex, dimeric water clusters are H-bonded to carboxylate O atoms forming both left- and right-handed helices. These helices are further H-bonded to form a tubular coordination polymer. It crystallizes in the monoclinic space group P2₁/a with a = 14.235(5), b = 23.097(4), c = 15.542(6) Å, β = 114.392(5)°, V = 4654(2) Å³, Z = 4, R₁ = 0.0422, wR₂ = 0.0992, S = 0.899. When pyridine is used in place of aqueous pyridine, a new coordination polymer, {Cu(cda)(py)}_n(2) is formed that crystallizes in the monoclinic space group P2₁/c with a = 12.391(5), b = 12.770(5), c = 7.135(5) Å, β = 95.155(5)°, V = 1124(1) Å³, Z = 4, R₁ = 0.0415, wR₂ = 0.0882, S = 1.190. The structure of 2 consists of carboxylate-bridged [Cu(cda)(py)] units extending as a zigzag infinite chain where each metal ion shows square-pyramidal geometry. Variable temperature magnetic susceptibility measurements in the temperature range, 2-300 K for 2 is also reported.     

Access to hybrid supramolecular salen-porphyrin assemblies via a selective in situ transmetalation-metalation self-assembly sequence

New supramolecular hybrid assemblies have been selectively prepared starting off with stoichiometric mixtures of pyridine-tagged Zn(salphen) and non-metalated porphyrin ligands in the presence of suitable metal acetates. This one-pot procedure leads to in situ transmetalation of the salen unit, metalation of the porphyrin ligand by the released Zn(OAc)₂ and subsequent heterometallic assembly formation between the metallosalen and metalloporphyrin components via Zn-N_pyr coordination motifs. The reactions were followed by NMR spectroscopy and MALDI-TOF mass spectrometry, and for one of the Zn(salphen) building blocks the X-ray molecular structure is reported.     

Synthetic fragments of plant polysaccharides as tools for cell wall biology

A sustainable bioeconomy that includes increased agricultural productivity and new technologies to convert renewable biomass to value-added products may help meet the demands of a growing world population for food, energy and materials. The potential use of plant biomass is determined by the properties of the cell walls, consisting of polysaccharides, proteins, and the polyphenolic polymer lignin. Comprehensive knowledge of cell wall glycan structure and biosynthesis is therefore essential for optimal utilization. However, several areas of plant cell wall research are hampered by a lack of available pure oligosaccharide samples that represent structural features of cell wall glycans. Here, we provide an update on recent chemical syntheses of plant cell wall oligosaccharides and their application in characterizing plant cell wall-directed antibodies and carbohydrate-active enzymes including glycosyltransferases and glycosyl hydrolases, with a particular focus on glycan array technology.     

The formation of a novel supramolecular structure by amyloid of poly-L-glutamic acid

Polyglutamic acid (PE) has been shown to form amyloid fibrils in vitro under pH value of 4.0. However, under the pH of 2.0, a further self-association process resulting in a novel supramolecular structure was observed. These supramolecular assemblies had diameters ranging from 1 to 20 μm and lengths up to several hundred microns, which were significantly larger than those of typical “amyloid fibrils”. The existence of amyloid-like structure within these assemblies was confirmed with Fourier transform infrared spectroscopy and Thioflavin T fluorescence assay. The aggregation process of PE was studied by direct observation of electronic microscopy. The supramolecular assemblies appeared to be formed in a hierarchical process in which the preformed amyloid-like subunits self-assembled into higher-order assemblies in a well-organized pattern.     

Using Lewis acidity differences in chelating ligands to control molecular structure and supramolecular assembly of Cu(II) complexes

The electronic effects of the fluorine atoms in hfacac (hexafluoroacetylacetonato) compared with acac (acetylacetonato) in Cu(II) complexes are used to control the molecular and supramolecular structure of Cu(II) compounds. While bis(acac)Cu(II) (acac = acetylacetonato) is known to be able to have a fifth-position coordination, bis(hfacac)Cu(II), (hfacac = hexafluoroacetylacetonato) may have two extra ligands. This, together with the reliable “supramolecular reagent” isonicotinamide, as the additional ligand, are used to go from a zero-dimension structure, with Cu-acac, to an extended supramolecular two-dimension network, with Cu-hfacac. The molecular and crystal structure of bis(acetylacetonato-O,O′)-(isonicotinamide-N) copper(II), 1, and bis(hexafluoroacetylacetonato-O,O′)-trans-bis(isonicotinamide-N) copper(II), 2, are reported.     

Design and DNA-binding of metallo-supramolecular cylinders conjugated to peptides

Di-nuclear metallo-supramolecular “cylinders”, based on bis-pyridylimine ligands, are end-functionalised with short peptides. The design and synthesis of one tetra-cationic triple-stranded (iron(II)) and three di-cationic double-stranded (copper(I) or silver(I)) cylinder-peptide conjugates are described. DNA-binding experiments, using circular and linear dichroism spectroscopies, confirm the binding and indicate that the iron(II) complexes cause DNA to bend or coil. Artificial nuclease activity by the copper(I) complexes is demonstrated by gel electrophoresis studies.     

Spatial distribution of mammalian cells dictated by material surface chemistry

Anisotropic cell culture surfaces patterned with amino and alkylsilanes can guide cell distribution and provide an approach to study important processes involved in tissue engineering, such as cell attachment and locomotion. By combining photolithographic and silane coupling techniques, glass coverslips were patterned with either n-octadecyldimethylchlorosilane (ODDMS) or dimethyldichlorosilane (DMS), and N-(2-aminoethyl)-3-aminopropyl-trimethoxysilane (EDS). The alkylsilanes, theoretically, have similar methyl and methylene groups exposed at the surface but different structures, with DMS being amorphous and ODDMS ordered. Neuroblastoma cells, osteosarcoma cells, and fibroblasts plated on surfaces patterned with EDS/ODDMS and EDS/DMS specifically localized on the EDS regions, but distributed randomly on ODDMS/DMS patterned surfaces. The preferential assembly of cells onto EDS regions did not depend on the structure of the adjacent alkylsilane regions and was a time-dependent process. Angle dependent x-ray photoelectron spectroscopy (XPS) and contact angle measurements indicated that EDS was immobilized on glass as a fractional hydrophilic monolayer, and ODDMS and DMS were bound as patchy amorphous hydrophobic multilayers. Neither surface coverage nor thickness of the overlayer seemed to be as important as surface chemistry, or charge, in guiding mammalian cell distribution. These results are consistent with the concept that mammalian cells attach to and are guided by positively charged surfaces.     

Cyclic assemblies formed by metal ions, pyrimidines and isogeometrical heterocycles: DNA binding properties and antitumour activity

In this contribution, we discuss the use of simple pyrimidine derivatives and geometrically related heterocycles in combination with protected metal ions to build cyclic polynuclear coordination assemblies. The resulting assemblies range from conformationally rigid triangles to corrugated octagons with positively charged cavities and surfaces that can interact with anionic species in a supramolecular fashion. Special attention has been focussed to the supramolecular interaction of these systems towards mononucleotides and DNA as a possible novel interaction of DNA binding metallo-drugs. The results show that these systems efficiently interact with both mononucleotides and ds-DNA. The molecular recognition of ds-DNA leads to significant conformational changes, however, this interaction gives only rise to moderate cytotoxic effects towards tumour cell lines.     

Use of acid-base and redox chemistry to synthesize cobalt(III) and iron(III) complexes of a partially deprotonated triprotic imidazole-containing Schiff base ligand: Hydrogen bound 1D linear homochiral and zig-zag heterochiral supramolecular complexes

Aerial reaction of cobalt(II) perchlorate with H₃(1) [H₃(1) is the tripodal ligand derived from the condensation of tris(2-aminoethyl)amine with three equivalents of imidazole-2-carboxaldehyde] in methanol and [FeH₃(1)(ClO₄)₂] with Fe(1) in acetonitrile results in the formation of [CoH₂L](ClO₄)₂·H₂O and [FeHL]ClO₄·CH₃CN, respectively. Mössbauer spectroscopy and variable temperature magnetic susceptibility indicate that [FeHL]ClO₄·CH₃CN is a low spin iron(III) species. Both complexes were characterized by EA, IR, and single crystal structure determinations. Both complexes crystallize in the centrosymmetric monoclinic space group, P2₁/c, so both enantiomers of the chiral complex are present. The supramolecular features of these complexes, caused by the partial deprotonation of the ligand and the resultant formation of imidazole-H···imidazolate hydrogen bonds, are different. [FeHL]⁺ forms hydrogen bonds with molecules from adjacent cells of like chirality. This results in a linear homochiral array of iron complexes. In contrast, [CoH₂L]²⁺ forms hydrogen bonds with a molecule from the same cell and one from another cell resulting in an 1D alternating heterochiral zig-zag chain.     

Click chemistry armed enzyme-linked immunosorbent assay to measure palmitoylation by hedgehog acyltransferase

Hedgehog signaling is critical for correct embryogenesis and tissue development. However, on maturation, signaling is also found to be aberrantly activated in many cancers. Palmitoylation of the secreted signaling protein sonic hedgehog (Shh) by the enzyme hedgehog acyltransferase (Hhat) is required for functional signaling. To quantify this important posttranslational modification, many in vitro Shh palmitoylation assays employ radiolabeled fatty acids, which have limitations in terms of cost and safety. Here we present a click chemistry armed enzyme-linked immunosorbent assay (click–ELISA) for assessment of Hhat activity through acylation of biotinylated Shh peptide with an alkyne-tagged palmitoyl-CoA (coenzyme A) analogue. Click chemistry functionalization of the alkyne tag with azido-FLAG peptide allows analysis through an ELISA protocol and colorimetric readout. This assay format identified the detergent n-dodecyl β-d-maltopyranoside as an improved solubilizing agent for Hhat activity. Quantification of the potency of RU-SKI small molecule Hhat inhibitors by click–ELISA indicated IC₅₀ values in the low- or sub-micromolar range. A stopped assay format was also employed that allows measurement of Hhat kinetic parameters where saturating substrate concentrations exceed the binding capacity of the streptavidin-coated plate. Therefore, click–ELISA represents a nonradioactive method for assessing protein palmitoylation in vitro that is readily expandable to other classes of protein lipidation.     

Illuminating the wall: Using click chemistry to image pectins in Arabidopsis cell walls

Plant cell walls are the most abundant biomaterials on Earth and serve a multitude of purposes in human society. These complex extracellular matrices are mainly composed of polysaccharides, including cellulose, hemicelluloses, and pectins, which cannot be cytologically examined using conventional techniques. Click chemistry, which exploits a bio-orthogonal cycloaddition reaction between alkynyl and azido groups, has proven to be useful for the metabolic incorporation and detection of modified sugars in polysaccharides in animals, fungi, and bacteria, but its use to interrogate the biosynthesis or dynamics of plant cell walls has not been previously reported. Recently, we found that an alkynylated analog of fucose can be metabolically incorporated into Arabidopsis thaliana cell walls and click labeled with fluorescent probes, facilitating imaging of cell wall carbohydrates. Despite the presence of fucose in several classes of wall polysaccharides, fucose-alkyne was primarily incorporated into rhamnogalacturonan-I, a type of pectin. Using timecourse and pulse-labeling experiments, we observed the dynamics of pectin delivery and reorganization in expanding cell walls. The use of click chemistry to investigate plant cell wall architecture should help bridge the gap between biochemical characterization of isolated cell wall components and an understanding of how those components interact in intact cell walls.     

人工合成多肽检测抗HIV－1和HIV－2抗体的研究

采用固相法合成ＨＩＶ－１和ＨＩＶ－２两个多肽,建立了用混合多肽为包被抗原检测ＨＩＶ－１和ＨＩＶ－２感染的间接酶联免疫吸附法。检测４６份抗ＨＩＶ－１和ＨＩＶ－２抗体阳性血清标本以及９４份对照血清标本,与ＵＢＩ试剂比较,其阳性符合率为９７．８％,阴性符合率为１００％,总符合率为９９．３％。实验结果表明,此法可用于ＨＩＶ－１和ＨＩＶ－２感染的检测。     

Food selection by the silver leaf monkey,Trachypithecus auratus sondaicus,in relation to plant chemistry

Summary Samples of leaves and fruits exploited as food items byTrachypithecus auratus sondaicus were analysed for nitrogen content, acid detergent fibre (ADF), pepsin cellulase digestibility (CDIG), condensed tannins (CT), total phenolics (TP) and protein precipitation capacity (PP) and compared with fruits and leaves not eaten. Differences in chemical measures for items eaten and not eaten were not statistically significant but trends indicate that leaves may have been selected for their lower fibre content and greater digestibility. Fruits eaten also had a higher mean level of CDIG and lower mean level of ADF than fruits not eaten but these measures are not considered to be of major importance in fruit selection as CDIG was lower and ADF higher in fruits eaten than in leaves eaten. Levels of CT, TP and PP capacity were higher in fruits eaten than in fruits not eaten but lower in leaves eaten than in leaves not eaten. The role of tannins and phenolics in food selection is discussed. Leaves (and fruits) were not strongly selected on the basis of protein content. Approximately half the dietary intake ofT. auratus sondaicus was leaves, a protein-rich food source. Possibly, protein levels in foliage at Pangandaran were sufficient that selection for this nutrient was not required. A nutrient other than protein (for example, soluble carbohydrates) may have been maximised through food selection. The protein/ADF ratio may provide an indicator of the acceptability of foliage in a habitat as potential food for a colobine. However, this ratio did not govern food selection byT. auratus sondaicus at Pangandaran.     

Approach to the mechanism of Zajdela's hepatoma cell growth inhibition induced by concanavalin A and phytohaemagglutinin

Cell growth of tumour ascites cell was inhibited by concanavalin A, phytohaemagglutinin and Ricinus lectin at 2–100 μg/ml. As expected, the Ricinus lectin inhibited the protein synthesis estimated by leucine incorporation and decreased thymidine incorporation, whereas concanavalin A and phytohaemagglutinin stimulate the uptake and the incorporation of both leucine and thymidine, and thus, synthesis of protein and DNA. Theses results suggest that different mechanisms are involved in the hepatoma cell growth inhibition by the lectins. This difference was not related to the kinetic characteristics of the lectin interactions with the cells whihc represent a first and necessary step. It was showed that concanavalin A and phytohaemagglutinin as well as chloroquine inhibited the ¹⁴C-labelled asialofetuin degradation. We can conclude that Ricinus lectic present a toxic effect whereas both concanavalin A and phytohaemagglutinin show an anti-protease activity.     

Approach to the Involvement of Influenza B Neuraminidase in the Cleavage of HA by Host Cell Protease Using Low pH-Induced Cell Fusion Reaction

ts7, a temperature-sensitive mutant defective in neuraminidase (NA) of influenza B/Kanagawa/73, lacks NA enzymatic activity at the nonpermissive temperature (37.5 C). When MDCK cells were infected with the mutant at the permissive temperature (32 C) and exposed to pH 5.2 medium, extensive cell fusion occurred. In contrast, at the nonpermissive temperature cells did not show cell fusion at all unless they were pretreated with trypsin, suggesting that at 37.5 C the hemagglutinin (HA) of ts7 is expressed at the cell surface in an uncleaved form. It was also found that the replacement of RNA segment 6 of ts7 with that of wild-type B/Lee resulted in the emergence of low pH-induced fusion activity as well as NA enzymatic activity at the incubation temperature of 37.5 C and that the addition of bacterial NA to the cultures infected with ts7 at 37.5 C early in infection brought about low pH-induced cell fusion. We suggest that the removal of neuraminic acid from the carbohydrate moiety of HA by NA is essential for the cleavage of HA by cellular protease.