A Binary Bivalent Supramolecular Assembly Platform Based on Cucurbit[8]uril and Dimeric Adapter Protein 14‐3‐3

Interactions between proteins frequently involve recognition sequences based on multivalent binding events. Dimeric 14‐3‐3 adapter proteins are a prominent example and typically bind partner proteins in a phosphorylation‐dependent mono‐ or bivalent manner. Herein we describe the development of a cucurbit[8]uril (Q8)‐based supramolecular system, which in conjunction with the 14‐3‐3 protein dimer acts as a binary and bivalent protein assembly platform. We fused the phenylalanine–glycine–glycine (FGG) tripeptide motif to the N‐terminus of the 14‐3‐3‐binding epitope of the estrogen receptor α (ERα) for selective binding to Q8. Q8‐induced dimerization of the ERα epitope augmented its affinity towards 14‐3‐3 through a binary bivalent binding mode. The crystal structure of the Q8‐induced ternary complex revealed molecular insight into the multiple supramolecular interactions between the protein, the peptide, and Q8.     

Cucurbituril‐mediated immobilization of fluorescent proteins on supramolecular biomaterials

The reversible introduction of functionality at material surfaces is of interest for the development of functional biomaterials. In particular, the use of supramolecular immobilization strategies facilitates mild reaction and processing conditions, as compared to other covalent analogues. Here, the engineering of multicomponent supramolecular materials, beyond the use of a single supramolecular entity is proposed. Cucurbit[8]uril (Q8) mediated host–guest chemistry is combined with hydrogen bonding supramolecular 2‐ureido‐4‐pyrimidinone (UPy)‐based materials. The modular incorporation of a UPy‐additive that presents one guest to incorporate into the Q8 host allows for selective supramolecular functionalization at the water–polymer material interface. Supramolecular ternary complex formation at the material surface was studied by X‐ray photoelectron spectroscopy, which as a result of large overlap in atomic composition of the different components showed minor changes is surface composition upon complex formation. Surface MALDI‐ToF MS measurements revealed useful insights in the formation of complexes. Protein immobilization was monitored using both fluorescence spectroscopy and quartz crystal microbalance with dissipation monitoring, which successfully demonstrated ternary complex formation. Although proteins could selectively be immobilized onto the surfaces, control of the system's stability remains a challenge as a result of the dynamicity of the host–guest assembly. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55, 3607–3616     

Genetically Encoded Bioluminescent Indicator for ERK2 Dimer in Living Cells

In this study, a genetically encoded bioluminescent indicator for ERK2 dimer was developed with the split Renilla luciferase complementation method, in which the formation of ERK2 dimer induces a spontaneous emission of bioluminescence in living cells. In response to extracellular stimuli, such as epidermal growth factor (EGF) or 17β‐estradiol (E2), extracellular signal‐regulated kinase 2 (ERK2) is phosphorylated by its upstream kinase MEK, and also phosphorylates its substrates in various regions of the cell, including the nucleus. Phosphorylated ERK2 is led to form its dimer, thereby transporting itself into the nucleus. We demonstrated with the indicator that stimulation with EGF or E2 induces the formation of ERK2 dimer in living MCF‐7 cells. The dynamics of this dimer formation was examined and discussed.     

A Binary Bivalent Supramolecular Assembly Platform Based on Cucurbit[8]uril and Dimeric Adapter Protein 14-3-3

Interactions between proteins frequently involve recognition sequences based on multivalent binding events. Dimeric 14-3-3 adapter proteins are a prominent example and typically bind partner proteins in a phosphorylation-dependent mono- or bivalent manner. Herein we describe the development of a cucurbit[8]uril (Q8)-based supramolecular system, which in conjunction with the 14-3-3 protein dimer acts as a binary and bivalent protein assembly platform. We fused the phenylalanine–glycine–glycine (FGG) tripeptide motif to the N-terminus of the 14-3-3-binding epitope of the estrogen receptor α (ERα) for selective binding to Q8. Q8-induced dimerization of the ERα epitope augmented its affinity towards 14-3-3 through a binary bivalent binding mode. The crystal structure of the Q8-induced ternary complex revealed molecular insight into the multiple supramolecular interactions between the protein, the peptide, and Q8.     

Directed Improvement of Luciferin Regenerating Enzyme Binding Properties: Implication of Some Conserved Residues in Luciferin‐Binding Domain

Luciferin regenerating enzyme (LRE) contributes to in vitro recycling of d ‐luciferin to produce persistent and longer light emission by luciferase. Luciferin binding domains I and II among LREs regarded as potential candidates for luciferin‐binding sites. In this study, for the first time, amino acids T69, G75 and K77 located at luciferin binding domain I of LRE from L. turkestanicus (T‐LRE) substituted by using site‐directed mutagenesis. Single mutant T⁶⁹R increased luciferase light output more than two‐fold over a longer time in comparison with a wild‐type and other mutants of T‐LRE. Nevertheless, double mutant (K⁷⁷E/T⁶⁹R) increased the amount of bioluminescent signal more than two‐fold over a short time. In addition, G⁷⁵E, K⁷⁷E and G⁷⁵E/T⁶⁹R mutants did not improve luciferin–luciferase in vitro bioluminescence. Based on our results, addition of K⁷⁷E/G⁷⁵E and K⁷⁷E/G⁷⁵E/T⁶⁹R mutants caused intermediate changes in bioluminescence from in vitro luciferin–luciferase reaction. These findings indicated that the amino acids in question are possible to be located within T‐LRE active site. It may also be suggested that substituted Arg69 (Arg218) plays an important role in luciferin binding and the existence of Gly75 as well as Lys77 is essential for T‐LRE which has already evolved to have different functions in nature.     

In Situ Spatial Complementation of Aptamer‐Mediated Recognition Enables Live‐Cell Imaging of Native RNA Transcripts in Real Time

Direct cellular imaging of the localization and dynamics of biomolecules helps to understand their function and reveals novel mechanisms at the single‐cell resolution. In contrast to routine fluorescent‐protein‐based protein imaging, technology for RNA imaging remains less well explored because of the lack of enabling technology. Herein, we report the development of an aptamer‐initiated fluorescence complementation (AiFC) method for RNA imaging by engineering a green fluorescence protein (GFP)‐mimicking turn‐on RNA aptamer, Broccoli, into two split fragments that could tandemly bind to target mRNA. When genetically encoded in cells, endogenous mRNA molecules recruited Split‐Broccoli and brought the two fragments into spatial proximity, which formed a fluorophore‐binding site in situ and turned on fluorescence. Significantly, we demonstrated the use of AiFC for high‐contrast and real‐time imaging of endogenous RNA molecules in living mammalian cells. We envision wide application and practical utility of this enabling technology to in vivo single‐cell visualization and mechanistic analysis of macromolecular interactions.     

Split-luciferase complementary assay: applications,recent developments,and future perspectives

Bioluminescent systems are considered as potent reporter systems for bioanalysis since they have specific characteristics, such as relatively high quantum yields and photon emission over a wide range of colors from green to red. Biochemical events are mostly accomplished through large protein machines. These molecular complexes are built from a few to many proteins organized through their interactions. These protein–protein interactions are vital to facilitate the biological activity of cells. The split-luciferase complementation assay makes the study of two or more interacting proteins possible. In this technique, each of the two domains of luciferase is attached to each partner of two interacting proteins. On interaction of those proteins, luciferase fragments are placed close to each other and form a complemented luciferase, which produces a luminescent signal. Split luciferase is an effective tool for assaying biochemical metabolites, where a domain or an intact protein is inserted into an internally fragmented luciferase, resulting in ligand binding, which causes a change in the emitted signals. We review the various applications of this novel luminescent biosensor in studying protein–protein interactions and assaying metabolites involved in analytical biochemistry, cell communication and cell signaling, molecular biology, and the fate of the whole cell, and show that luciferase-based biosensors are powerful tools that can be applied for diagnostic and therapeutic purposes.     

Tyr72 and Tyr80 are Involved in the Formation of an Active Site of a Luciferase of Copepod Metridia longa

Luciferase of copepod Metridia longa (MLuc) is a naturally secreted enzyme catalyzing the oxidative decarboxylation of coelenterazine with the emission of light. To date, three nonallelic isoforms of different lengths (17–24 kDa) for M. longa luciferase have been cloned. All the isoforms are single‐chain proteins consisting of a 17‐residue signal peptide for secretion, variable N‐terminal part and conservative C‐terminus responsible for luciferase activity. In contrast to other bioluminescent proteins containing a lot of aromatic residues which are frequently involved in light emission reaction, the C‐terminal part of MLuc contains only four Phe, two Tyr, one Trp and two His residues. To figure out whether Tyr residues influence bioluminescence, we constructed the mutants with substitution of Tyr to Phe (Y72F and Y80F). Tyrosine substitutions do not eliminate the ability of luciferase to bioluminescence albeit significantly reduce relative specific activity and change bioluminescence kinetics. In addition, the Tyr replacements have no effect on bioluminescence spectrum, thereby indicating that tyrosines are not involved in the emitter formation. However, as it was found that the intrinsic fluorescence caused by Tyr residues is quenched by a reaction substrate, coelenterazine, in concentration‐dependent manner, we infer that both tyrosine residues are located in the luciferase substrate‐binding cavity.     

Covalent split protein fragment-DNA hybrids generated through N-terminus-specific modification of proteins by oligonucleotides

Semisynthetic protein-DNA hybrid molecules have recently attracted much attention as valuable tools for bioanalytical chemistry and nanobiotechnology. Here we describe a synthetic method for conjugating oligonucleotides to the N-terminus of recombinant proteins. Our strategy involves the conversion of amine-terminated oligonucleotides to thioester-functionalized oligonucleotides by using a bifunctional reagent bearing an N-hydroxysuccinimide ester and benzyl thioester group, followed by native chemical ligation with proteins containing an N-terminal cysteine. We applied this technique to construct split luciferase fragment-DNA hybrid systems in which the catalytic activity of split luciferase is restored by the re-assembly of each fragment through a specific DNA-protein or DNA-DNA interaction. Split protein fragment-DNA hybrids will offer new opportunities to explore the potential of protein-DNA conjugates for various applications.     

Supramolecular Zinc Phthalocyanine–Imidazolyl Perylenediimide Dyad and Triad: Synthesis,Complexation, and Photophysical Studies

Two new supramolecular architectures based on zinc phthalocyanine (Pc) and imidazolyl‐substituted perylenediimide (PDI), ZnPc/DImPDI/ZnPc 1 and ZnPc/ImPDI 2 , have been prepared. A strong electron‐donor, 8 , which contained eight tert‐octylphenoxy groups was synthesized to ensure high solubility, thereby reducing aggregation in solution and providing σ‐donor features while avoiding regioisomeric mixtures. Also, PDI units were functionalized with tert‐octylphenoxy groups at the bay positions, which provide solubility to avoid aggregation in solution, together with one and two imidazole moieties in the amide position, 6 and 4 , respectively, to be able to strongly coordinate with the ZnPc complex. Supramolecular complexation studies by ¹H NMR spectroscopy and ESI‐MS demonstrate a high coordinative binding constant between imidazole‐substituted 4 or 6 and 8 . The same results were confirmed by UV/Vis and fluorescence titration studies. UV/Vis titration studies revealed the formation of a 1:1 complex ZnPc/ImPDI 2 for the systems 8 and 6 and a 2:1 complex ZnPc/DImPDI/ZnPc 1 for the interaction of 8 and 4 . The binding constant in both cases was determined to be on the order of 10⁵ M ⁻¹. Femtosecond laser flash photolysis measurements provided a direct proof of the charge‐separated state within both supramolecular assemblies by observing the transient absorption band at 820 nm due to the zinc phthalocyanine radical cation. The lifetimes of charge‐separated states are (9.8±3) ns for triad 1 and (3±1) ns for dyad 2 . As far as we know, this is the first time that a radical ion pair has been detected in a supramolecular assembled ZnPc–PDI system and has obtained the longest lifetime of a charge‐separated state published for ZnPc–PDI assemblies.     

IBX Oxidation of Benzenedimethanols in the Presence of Cucurbit[8]uril

The cucurbit[8]uril (Q[8]) mediated oxidation of benzenedimethanols with o‐iodoxybenzoic acid (IBX) in aqueous solution has been investigated, and the results reveal the supramolecular catalysis depends on the electronic and geometric structure of substrate. In the cases of o‐benzenedimethanol ( 1a ) and m‐benzenedimethanol ( 1b ), the IBX oxidation could be obviously enhanced by the addition of Q[8] at different extent. There is no observation of the catalytic activity of Q[8] when p‐benzenedimethanol ( 1c ) is subjected to the IBX oxidation. The addition amount of Q[8] is discussed herein, and the addition of more than 10% mol catalyst cannot improve the oxidation much more. The investigation of host‐guest interactions by isothermal titration calorimetry implies the supramolecular catalysis is related to the formation of complexes between benzenedimethanols and cucurbit[8]uril.     

RNA detection using peptide-inserted <Emphasis Type="Italic">Renilla</Emphasis> luciferase

A novel complementation system with short peptide-inserted-Renilla luciferase (PI-Rluc) and split-RNA probes was constructed for noninvasive RNA detection. The RNA binding peptides HIV-1 Rev and BIV Tat were used as inserted peptides. They display induced fit conformational changes upon binding to specific RNAs and trigger complementation or discomplementation of Rluc. Split-RNA probes were designed to reform the peptide binding site upon hybridization with arbitrarily selected target RNA. This set of recombinant protein and split-RNA probes enabled a high degree of sensitivity in RNA detection. In this study, we show that the Rluc system is comparable to Fluc, but that its detection limit for arbitrarily selected RNA (at least 100 pM) exceeds that of Fluc by approximately two orders of magnitude.     

Cucurbit[n]urils (n=7, 8) binding of camptothecin and the effects on solubility and reactivity of the anticancer drug

The interaction between cucurbit[n]uril (n = 7, 8)(Q[n]) with two forms namely lactone modality and carboxylate modality of anticancer drug camptothecin (CPT) was studied. The results revealed that the combination of Q[n] with the lactone form of CPT was observed by electronic absorption spectroscopy, fluorescence spectroscopy and ¹H NMR technique in the acid solution (pH 2) and the total stability constants β were also obtained by Job plot with a host:guest ratio of 2:1; while in the phosphate buffer solution (pH 7.4), only Q[8] bound the carboxylate form of CPT in ratio 1:1, but no obvious interaction between Q[7] and the carboxylate form of CPT was observed. The solubility of CPT was enhanced up to about 70 and 8 times at pH 2 due to the formation of interaction complexes with Q[7] and Q[8], respectively, by using phase solubility method. The cytotoxicity tests revealed that compared with the free CPT, the complexes of Q[n] and CPT had the same cytotoxic activity on the human lung cancer cell line A549 and murine macrophage cell line P388D1 and the moderate depressed activity on human leukaemia cell line K562.     

Firefly Luciferase‐based Fusion Proteins and their Applications in Bioanalysis

Firefly luciferase is widely used in molecular biology and bioanalytical systems as a reporter molecule due to the high quantum yield of the bioluminescence, availability of stable mutant forms of the enzyme with prescribed spectral characteristics and abundance of bacterial expression systems suitable for production of recombinant proteins in limitless quantities. In this review, we described fusion proteins of luciferase with biotin‐binding domain and streptavidin, with proteins A and G, antibodies, with DNA‐ and RNA‐binding proteins, as well as fusion proteins designed for BRET systems. The firefly luciferase‐based fusion proteins are represented as an effective tool for the development of different bioanalytical systems such as (1) systems in which luciferase is attached to the surface of the target and the bioluminescence signal is detected from the specific complexes formed; (2) BRET‐based systems, in which the specific interaction induces changes in the bioluminescence spectrum; and (3) systems that use modified or split luciferases, in which the luciferase activity changes under the action of the analyte. All these systems have wide application in biochemical analysis of physiologically important compounds, for the detection of pathogenic bacteria and viruses, for evaluation of protein–protein interactions, assaying of metabolites involved in cell communication and cell signaling.     

Bioactivity‐based ultra‐performance liquid chromatography‐coupled quadrupole time‐of‐flight mass spectrometry for NF‐κB inhibitors identification in Chinese Medicinal Preparation Bufei Granule

Traditional Chinese medicine (TCM) preparations have become effective treatments for many diseases. However, their active ingredients are still uncertain and difficult to identify. In this study, we propose a strategy that integrates ultra‐performance liquid chromatography/quadrupole‐time‐of‐flight mass spectrometry (UPLC/Q‐TOF‐MS) and bioactive (NF‐κB inhibitor) luciferase reporter assay systems for the rapid determination of various anti‐inflammatory compounds of TCM preparations. In this way, Bufei Granule (BFG), a TCM preparation used for the clinical therapy of asthma, was analyzed by the two ways of component identification and activity detection. Potential anti‐inflammatory constituents were screened by NF‐κB activity assay systems and simultaneously identified according to the mass spectrometry data. Three structural types of NF‐κB inhibitors (caffeic acid derivatives, flavonoids and Pentacyclic triterpenes) were characterized. Further cytokine detection confirmed the anti‐inflammatory effects of the potential NF‐κB inhibitors. Compared with conventional chromatographic separation and inhibitory activity detection, integrating UPLC/Q‐TOF‐MS identification and virtual validation was more convenient and more reliable. This strategy clearly demonstrates that MS data‐based fingerprinting is a meaningful tool not only in identifying constituents in complex matrix but also in directly screening for powerful trace ingredients in TCM preparations. Copyright © 2016 John Wiley & Sons, Ltd.     

Photochemical Regulation of Gene Expression Using Caged siRNAs with Single Terminal Vitamin E Modification

Caged siRNAs with a single photolabile linker and/or vitamin E (vitE) modification at the 5′ terminal were rationally designed and synthesized. These virtually inactive caged siRNAs were successfully used to photoregulate both firefly luciferase and GFP gene expression in cells with up to an 18.6‐fold enhancement of gene silencing activity, which represents one of the best reported photomodulation of gene silencing efficiencies to date. siRNA tracking and vitE competition experiments indicated that the inactivity of vitE‐modified siRNAs was not due to the bulky moiety of vitE; rather, the involvement of vitE‐binding proteins has a large contribution to caged siRNA inactivation by preventing the dissociation of siRNA/lipo complexes and/or siRNA release. Further patterning experiments revealed the ability to spatially regulate gene expression through simple light irradiation.     

A Novel Catalytic Function of Synthetic IgG‐Binding Domain (Z Domain) from Staphylococcal Protein A: Light Emission with Coelenterazine

The synthetic IgG‐binding domain (Z domain) of staphylococcal protein A catalyzes the oxidation of coelenterazine to emit light like a coelenterazine‐utilizing luciferase. The Z domain derivatives (ZZ‐gCys, Z‐gCys and Z‐domain) were purified and the luminescence properties were characterized by comparing with coelenterazine‐utilizing luciferases, including Renilla luciferase, Gaussia luciferase and the catalytic 19 kDa protein of Oplophorus luciferase. Three Z domain derivatives showed luminescence activity with coelenterazine and the order of the initial maximum intensity of luminescence was ZZ‐gCys (100%) > Z‐gCys (36.8%) > Z‐domain (1.1%) > bovine serum albumin (BSA; 0.9%) > staphylococcal protein A (0.1%) and the background value of coelenterazine (0.1%) in our conditions. The luminescence properties of ZZ‐gCys showed the similarity to that of Gaussia luciferase, including the luminescence pattern, the emission spectrum, the stimulation by halogen ions and nonionic detergents and the substrate specificity for coelenterazine analogues. In contrast, the luminescence properties of Z‐gCys were close to the catalytic 19 kDa protein of Oplophorus luciferase. The catalytic region of the Z domain for the luminescence reaction might be different from the IgG‐binding region of the Z domain.     

Luciferin‐Regenerating Enzyme Crystal Structure Is Solved but its Function Is Still Unclear

Contribution of luciferin‐regenerating enzyme (LRE) for in vitro recycling of D‐luciferin has been reported. According to crystal structure of LRE, it is a beta‐propeller protein which is a type of all β‐protein architecture. In this overview, reinvestigation of the luciferase‐based LRE assays and its function is reported. Until now, sequence of LRE genes from four different species of firefly has been reported. In spite of previous reports, T‐LRE (from Lampyris turkestanicus) was cloned and expressed in Escherichia coli as well as Pichia pastoris in a nonsoluble form as inclusion body. According to recent investigations, bioluminescent signal of soluble T‐LRE–luciferase‐coupled assay increased and then reached an equilibrium state in the presence of D‐cysteine. In addition, the results revealed that both D‐ and L‐cysteine in the absence of T‐LRE caused a significant increase in bioluminescence intensity of luciferase over a long time. Based on activity measurements and spectroscopic results, D‐cysteine increased the activity of luciferase due to its redox potential and induction of conformational changes in structure and kinetics properties. In conclusion, in spite of previous reports on the effect of LRE (at least T‐LRE) on luciferase activity, most of the increase in luciferase activity is caused by direct effect of D‐cysteine on structure and activity of firefly luciferase. Moreover, bioinformatics analysis cannot support the presence of LRE in peroxisome of photocytes in firefly lanterns.     

Dynamic Interfacial Adhesion through Cucurbit[n]uril Molecular Recognition

Supramolecular building blocks, such as cucurbit[n]uril (CB[n])‐based host–guest complexes, have been extensively studied at the nano‐ and microscale as adhesion promoters. Herein, we exploit a new class of CB[n]‐threaded highly branched polyrotaxanes (HBP‐CB[n]) as aqueous adhesives to macroscopically bond two wet surfaces, including biological tissue, through the formation of CB[8] heteroternary complexes. The dynamic nature of these complexes gives rise to adhesion with remarkable toughness, displaying recovery and reversible adhesion upon mechanical failure at the interface. Incorporation of functional guests, such as azobenzene moieties, allows for stimuli‐activated on‐demand adhesion/de‐adhesion. Macroscopic interfacial adhesion through dynamic host–guest molecular recognition represents an innovative strategy for designing the next generation of functional interfaces, biomedical devices, tissue adhesives, and wound dressings.     

A Study of the Interaction Between Cucurbit[8]uril and Alkyl‐Substituted 4‐Pyrrolidinopyridinium Salts

The interaction between cucuribit[8]uril (Q[8]) and a series of 4‐pyrrolidinopyridinium salts bearing aliphatic substituents at the pyridinium nitrogen, namely 4‐(C₄H₈N)C₅H₅NRBr, where R=Et (g1), n‐butyl (g2), n‐pentyl (g3), n‐hexyl (g4), n‐octyl (g5), n‐dodecyl (g6), has been studied in aqueous solution by ¹H NMR spectroscopy, electronic absorption spectroscopy, isothermal titration calorimetry and mass spectrometry. Single crystal X‐ray diffraction revealed the structure of the host–guest complexes for g1, g2, g3, and g5. In each case, the Q[8] contains two guest molecules in a centrosymmetric dimer. The orientation of the guest molecule changes as the alkyl chain increases in length. Interestingly, in the solid state, the inclusion complexes identified are different from those observed in solution, and furthermore, in the case of g3, Q[8] exhibits two different interactions with the guest. In solution, the length of the alkyl chain plays a significant role in determining the type of host–guest interaction present.