Chemical Probes to Directly Profile Palmitoleoylation of Proteins

Palmitoleoylation is a unique fatty acylation of proteins in which a monounsaturated fatty acid, palmitoleic acid (C16:1), is covalently attached to a protein. Wnt proteins are known to be palmitoleoylated by cis‐Δ9 palmitoleate at conserved serine residues. O‐palmitoleoylation plays a critical role in regulating Wnt secretion, binding to the receptors, and in the dynamics of Wnt signaling. Therefore, protein palmitoleoylation is important in tissue homeostasis and tumorigenesis. Chemical probes based on saturated fatty acids, such as ω‐alkynyl palmitic acid (Alk‐14 or Alk‐C₁₆), have been used to study Wnt palmitoleoylation. However, such probes require prior conversion to the unsaturated fatty acid by stearoyl‐CoA desaturase (SCD) in cells, significantly decreasing their selectivity and efficiency for studying protein palmitoleoylation. We synthesized and characterized ω‐alkynyl cis‐ and trans‐palmitoleic acids (cis‐ and trans‐Alk‐14:1) as chemical probes to directly study protein palmitoleoylation. We found that cis‐Alk‐14:1 could more efficiently label Wnt proteins in cells. Interestingly, the DHHC family of palmitoyl acyltransferases can charge both saturated and unsaturated fatty acids, potentially using both as acyl donors in protein palmitoylation and palmitoleoylation. Furthermore, proteomic analysis of targets labeled by these probes revealed new cis‐ and trans‐palmitoleoylated proteins. Our studies provided new chemical tools and revealed new insights into palmitoleoylation in cell signaling.     

A DNA‐Encoded Library of Chemical Compounds Based on Common Scaffolding Structures Reveals the Impact of Ligand Geometry on Protein Recognition

A DNA‐encoded chemical library (DECL) with 1.2 million compounds was synthesized by combinatorial reaction of seven central scaffolds with two sets of 343×492 building blocks. Library screening by affinity capture revealed that for some target proteins, the chemical nature of building blocks dominated the selection results, whereas for other proteins, the central scaffold also crucially contributed to ligand affinity. Molecules based on a 3,5‐bis(aminomethyl)benzoic acid core structure were found to bind human serum albumin with a K_d value of 6 nm , while compounds with the same substituents on an equidistant but flexible l ‐lysine scaffold showed 140‐fold lower affinity. A 18 nm tankyrase‐1 binder featured l ‐lysine as linking moiety, while molecules based on d ‐Lysine or (2S,4S)‐amino‐l ‐proline showed no detectable binding to the target. This work suggests that central scaffolds which predispose the orientation of chemical building blocks toward the protein target may enhance the screening productivity of encoded libraries.     

Interrogating PP1 Activity in the MAPK Pathway with Optimized PP1-Disrupting Peptides

Protein phosphatase-1 (PP1)-disrupting peptides (PDPs) are selective chemical modulators of PP1 that liberate the active PP1 catalytic subunit from regulatory proteins; thus allowing the dephosphorylation of nearby substrates. We have optimized the original cell-active PDP3 for enhanced stability, and obtained insights into the chemical requirements for stabilizing this 23-mer peptide for cellular applications. The optimized PDP-Nal was used to dissect the involvement of PP1 in the MAPK signaling cascade. Specifically, we have demonstrated that, in human osteosarcoma (U2OS) cells, phosphoMEK1/2 is a direct substrate of PP1, whereas dephosphorylation of phosphoERK1/2 is indirect and likely mediated through enhanced tyrosine phosphatase activity after PDP-mediated PP1 activation. Thus, as liberators of PP1 activity, PDPs represent a valuable tool for identifying the substrates of PP1 and understanding its role in diverse signaling cascades.     

Genome-wide Identification and Characterization of FCS-Like Zinc Finger (FLZ) Family Genes in Maize (Zea mays) and Functional Analysis of ZmFLZ25 in Plant Abscisic Acid Response

FCS-like zinc finger family proteins (FLZs), a class of plant-specific scaffold of SnRK1 complex, are involved in the regulation of various aspects of plant growth and stress responses. Most information of FLZ family genes was obtained from the studies in Arabidopsis thaliana, whereas little is known about the potential functions of FLZs in crop plants. In this study, 37 maize FLZ (ZmFLZ) genes were identified to be asymmetrically distributed on 10 chromosomes and can be divided into three subfamilies. Protein interaction and subcellular localization assays demonstrated that eight typical ZmFLZs interacted and partially co-localized with ZmKIN10, the catalytic α-subunit of the SnRK1 complex in maize leaf mesophyll cells. Expression profile analysis revealed that several ZmFLZs were differentially expressed across various tissues and actively responded to diverse abiotic stresses. In addition, ectopic overexpression of ZmFLZ25 in Arabidopsis conferred hypersensitivity to exogenous abscisic acid (ABA) and triggered higher expression of ABA-induced genes, pointing to the positive regulatory role of ZmFLZ25 in plant ABA signaling, a scenario further evidenced by the interactions between ZmFLZ25 and ABA receptors. In summary, these data provide the most comprehensive information on FLZ family genes in maize, and shed light on the biological function of ZmFLZ25 in plant ABA signaling.     

Small‐Molecule Inhibitors of AF6 PDZ‐Mediated Protein–Protein Interactions

PDZ (PSD‐95, Dlg, ZO‐1) domains are ubiquitous interaction modules that are involved in many cellular signal transduction pathways. Interference with PDZ‐mediated protein–protein interactions has important implications in disease‐related signaling processes. For this reason, PDZ domains have gained attention as potential targets for inhibitor design and, in the long run, drug development. Herein we report the development of small molecules to probe the function of the PDZ domain from human AF6 (ALL1‐fused gene from chromosome 6), which is an essential component of cell–cell junctions. These compounds bind to AF6 PDZ with substantially higher affinity than the peptide (Ile‐Gln‐Ser‐Val‐Glu‐Val) derived from its natural ligand, EphB2. In intact cells, the compounds inhibit the AF6–Bcr interaction and interfere with epidermal growth factor (EGF)‐dependent signaling.     

A yeast surface display platform for plant hormone receptors: Toward directed evolution of new biosensors

Small-molecule biosensors have major applications in biotechnology and medicine but remain difficult to engineer. Plant hormone receptors represent an attractive platform for engineering such biosensors because their chemically induced dimerization architectures naturally decouple small-molecule sensing and sensor actuation. Rapid biosensor engineering will require quantitative high-throughput screening methods. Here we develop a yeast surface display (YSD) platform for the PYR1/HAB1 abscisic acid sensor of Arabidopsis thaliana. We extensively optimized PYR1 surface display, HAB1 purification, and binding reaction conditions. Our system reproduces previous results with wild-type and engineered receptors, and a mathematical analysis of the PYR1/HAB1 system allows us to infer all binding constants. Critically, we find that a previously engineered PYR1 receptor with altered ligand specificity binds HAB1 with identical affinity, suggesting that substantial reengineering of the PYR1 binding pocket does not compromise sensor actuation. This YSD platform for A. thaliana PYR1/HAB1 will facilitate future biosensor engineering efforts.     

Bottom‐up Design of Small Molecules that Stimulate Exon 10 Skipping in Mutant MAPT Pre‐mRNA

One challenge in chemical biology is to develop small molecules that control cellular protein content. The amount and identity of proteins are influenced by the RNAs that encode them; thus, protein content in a cell could be affected by targeting mRNA. However, RNA has been traditionally difficult to target with small molecules. In this report, we describe controlling the protein products of the mutated microtubule‐associated protein tau (MAPT) mature mRNA with a small molecule. MAPT mutations in exon 10 are associated with inherited frontotemporal dementia and Parkinsonism linked to chromosome 17 (FTDP‐17), an incurable disease that is directly caused by increased inclusion of exon 10 in MAPT mRNA. Recent studies have shown that mutations within a hairpin at the MAPT exon 10–intron junction decrease the thermodynamic stability of the RNA, increasing binding to U1 snRNP and thus exon 10 inclusion. Therefore, we designed small molecules that bind and stabilize a mutant MAPT by using Inforna, a computational approach based on information about RNA–small‐molecule interactions. The optimal compound selectively bound the mutant MAPT hairpin and thermodynamically stabilized its folding, facilitating exon 10 exclusion.     

The Alkylquinolone Repertoire of Pseudomonas aeruginosa is Linked to Structural Flexibility of the FabH‐like 2‐Heptyl‐3‐hydroxy‐4(1H)‐quinolone (PQS) Biosynthesis Enzyme PqsBC

Pseudomonas aeruginosa is a bacterial pathogen that causes life‐threatening infections in immunocompromised patients. It produces a large armory of saturated and mono‐unsaturated 2‐alkyl‐4(1H)‐quinolones (AQs) and AQ N‐oxides (AQNOs) that serve as signaling molecules to control the production of virulence factors and that are involved in membrane vesicle formation and iron chelation; furthermore, they also have, for example, antibiotic properties. It has been shown that the β‐ketoacyl‐acyl‐carrier protein synthase III (FabH)‐like heterodimeric enzyme PqsBC catalyzes the last step in the biosynthesis of the most abundant AQ congener, 2‐heptyl‐4(1H)‐quinolone (HHQ), by condensing octanoyl‐coenzyme A (CoA) with 2‐aminobenzoylacetate (2‐ABA), but the basis for the large number of other AQs/AQNOs produced by P. aeruginosa is not known. Here, we demonstrate that PqsBC uses different medium‐chain acyl‐CoAs to produce various saturated AQs/AQNOs and that it also biosynthesizes mono‐unsaturated congeners. Further, we determined the structures of PqsBC in four different crystal forms at 1.5 to 2.7 Å resolution. Together with a previous report, the data reveal that PqsBC adopts open, intermediate, and closed conformations that alter the shape of the acyl‐binding cavity and explain the promiscuity of PqsBC. The different conformations also allow us to propose a model for structural transitions that accompany the catalytic cycle of PqsBC that might have broader implications for other FabH‐enzymes, for which such structural transitions have been postulated but have never been observed.     

The effects of chemical structure and synthesis method on photodegradation of polypropylene

The effects of chemical structure and synthesis method on the photodegradation behavior of polypropylene (PP) were investigated in injection‐molded samples exposed to ultraviolet radiation (UV) at 60°C. For this purpose, three PP samples with different chemical structures were chosen: two homopolymerized PP samples (H₁P, synthesized by bulk polymerization; whereas H₂P was synthesized by Ziegler–Natta catalyst) and copolymerized PP sample (CP). The photodegradation was characterized by melt flow rate and mechanical properties and Fourier transform infrared spectroscopy, X‐ray photoelectron spectroscopy, and scanning electron microscopy. The results showed that CP possesses the most superior resistance to UV‐irradiation, followed by H₂P and then H₁P, which indicates that copolymerization with a small amount of ethylene monomer is an effective approach to obtain high stability of PP to UV‐irradiation, and synthesis methods of PP play an important role in the resistance to UV‐irradiation. Moreover, the effect of photodegradation on the thermal behaviors of H₂P was also investigated using X‐ray diffraction, differential scanning calorimetry, and dynamical mechanical thermal analysis. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 95: 270–279, 2005     

A High‐Throughput Screen for Chemical Inhibitors of Exocytic Transport in Yeast

Most of the components of the membrane and protein traffic machinery were discovered by perturbing their functions, either with bioactive compounds or by mutations. However, the mechanisms responsible for exocytic transport vesicle formation at the Golgi and endosomes are still largely unknown. Both the exocytic traffic routes and the signaling pathways that regulate these routes are highly complex and robust, so that defects can be overcome by alternate pathways or mechanisms. A classical yeast genetic screen designed to account for the robustness of the exocytic pathway identified a novel conserved gene, AVL9, which functions in late exocytic transport. We now describe a chemical‐genetic version of the mutant screen, in which we performed a high‐throughput phenotypic screen of a large compound library and identified novel small‐molecule secretory inhibitors. To maximize the number and diversity of our hits, the screen was performed in a pdr5Δ snq2Δ mutant background, which lacks two transporters responsible for pleiotropic drug resistance. However, we found that deletion of both transporters reduced the fitness of our screen strain, whereas the pdr5Δ mutation had a relatively small effect on growth and was also the more important transporter mutation for conferring sensitivity to our hits. In this and similar chemical‐genetic yeast screens, using just a single pump mutation might be sufficient for increasing hit diversity while minimizing the physiological effects of transporter mutations.     

Biodegradation Capability and Enzymatic Variation of Potentially Hazardous Polycyclic Aromatic Hydrocarbons—Anthracene and Pyrene by Anabaena fertilissima

This study encompasses the biodegradation capacity of Anabaena fertilissima to model PAH (Polycyclic Aromatic Hydrocarbon) compounds namely Anthracene (ANT) and Pyrene (PYR) at different LC₅₀ concentrations viz., 5.0 mg/L and 3.0 mg/L, respectively, on growth in terms of Chlorophyll-a and protein. Depletion in chlorophyll-a and protein content was registered with rise in PAHs concentration while the inhibition of nitrogen fixing enzymes such as nitrate reductase and glutamine synthetase activity was also concentration dependent and showed more sensitivity for high molecular weight aromatic compound PYR as compared to ANT. GC/MS analysis explained the degradation of ANT by 46% and PYR by 33%, at 5.0 mg/L and 3.0 mg/L, respectively. Moreover, the common degraded product for ANT was 2, 4-Dimethyl-1-heptene and for PYR it was 2, 3, 4-Trimethylhexane. Results indicate that PYR was more stable and recalcitrant compared to ANT. This study suggests that Anabaena fertilissima could be used for bioremediation of ANT and PYR pollution in surface waters and terrestrial environments.     

Efficient Total Chemical Synthesis of 13C=18O Isotopomers of Human Insulin for Isotope‐Edited FTIR

Isotope‐edited two‐dimensional Fourier transform infrared spectroscopy (2 D FTIR) can potentially provide a unique probe of protein structure and dynamics. However, general methods for the site‐specific incorporation of stable ¹³C=¹⁸O labels into the polypeptide backbone of the protein molecule have not yet been established. Here we describe, as a prototype for the incorporation of specific arrays of isotope labels, the total chemical synthesis—via a key ester insulin intermediate—of 97 % enriched [(1‐¹³C=¹⁸O)Phe^B24] human insulin: stable‐isotope labeled at a single backbone amide carbonyl. The amino acid sequence as well as the positions of the disulfide bonds and the correctly folded structure were unambiguously confirmed by the X‐ray crystal structure of the synthetic protein molecule. In vitro assays of the isotope labeled [(1‐¹³C=¹⁸O)Phe^B24] human insulin showed that it had full insulin receptor binding activity. Linear and 2 D IR spectra revealed a distinct red‐shifted amide I carbonyl band peak at 1595 cm^?1 resulting from the (1‐¹³C=¹⁸O)Phe^B24 backbone label. This work illustrates the utility of chemical synthesis to enable the application of advanced physical methods for the elucidation of the molecular basis of protein function.     

Synthesis of tris(2‐hydroxyethyl) isocyanurate homopolymer and its application in intumescent flame retarded polypropylene

A macromolecular homopolymer (named as Homo‐THEIC) was synthesized through self‐etherification of tris(2‐hydroxyethyl) isocyanurate (THEIC) molecules and used as charring agent. Its chemical structure was characterized by FTIR and ¹³C‐NMR. The charring agent was mixed with ammonium polyphosphate (APP) and applied in flame retarded polypropylene (PP). Results of UL‐94, LOI, and cone calorimeter test showed that the LOI of flame retarded PP can reach 32.8% and UL‐94 V‐0 rating can be achieved at 30 wt % loading. The heat release rate and smoke production rate during the combustion of PP were substantially reduced. TGA results indicated that the synergistic effect between APP and Homo‐THEIC existed and the addition of intumescent flame retardant (IFR) dramatically enhanced the thermal stability of PP. According to the results of TGA, SEM, TG‐FTIR, FTIR, and Raman, the char forming process of IFR can be separated into three stages: the formation of viscous phosphate ester (T _onset?330 °C), the expanding process along with the decomposition of phosphate ester and the release of a large amount of gases (330–480 °C), and the final formation of graphitic‐like char without any expanding feature (480–670 °C). © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2017 , 134 , 44663.     

Phosphatidylethanolamine‐Binding Proteins,Including RKIP,Exhibit Affinity for Phosphodiesterase‐5 Inhibitors

Identifying protein “interactors” of drugs is of great importance to understand their mode of action and possible cross‐reactivity to off‐target protein binders. In this study, we profile proteins that bind to PF‐3717842, a high‐affinity phosphodiesterase‐5 (PDE5) inhibitor, by using a refined affinity pulldown approach with PF‐3717842 immobilized beads. By performing these pulldowns in rat testis tissue lysate, we strongly and specifically enriched for PDE5 and a few other PDEs. In addition to these expected affinity‐enriched proteins we also detect rodent‐specific phosphatidylethanolamine‐binding protein 2 (PEBP2), as a putative binder to the PDE5 inhibitor. By using recombinant forms of the related murine mPEBP2, mPEBP1 and human hPEBP1 (also known as Raf kinase inhibitor protein or RKIP) we confirm that they all can bind strongly to immobilized as well as soluble PF‐3717842. As the phosphatidylethanolamine‐binding proteins are involved in various important signal transduction pathways, the synthetic PDE5 inhibitor used here might form a platform to synthesize enhanced binders/inhibitors of the family of PEBP proteins. Our approach shows how chemical proteomics might be used to profile the biochemical space (interactome) of small molecule inhibitors.     

Recent Progress in Strategies for the Creation of Protein‐Based Fluorescent Biosensors

The creation of novel bioanalytical tools for the detection and monitoring of a range of important target substances and biological events in vivo and in vitro is a great challenge in chemical biology and biotechnology. Protein‐based fluorescent biosensors—integrated devices that convert a molecular‐recognition event to a fluorescent signal—have recently emerged as a powerful tool. As the recognition units various proteins that can specifically recognize and bind a variety of molecules of biological significance with high affinity are employed. For the transducer, fluorescent proteins, such as green fluorescent protein (GFP) or synthetic fluorophores, are mostly adopted. Recent progress in protein engineering and organic synthesis allows us to manipulate proteins genetically and/or chemically, and a library of such protein scaffolds has been significantly expanded by genome projects. In this review, we briefly describe the recent progress of protein‐based fluorescent biosensors on the basis of their platform and construction strategy, which are primarily divided into the genetically encoded fluorescent biosensors and chemically constructed biosensors.