Sequential Binding Research Articles

The scaffold-protein IQGAP1 enhances and spatially restricts the actin-nucleating activity of Diaphanous-related formin 1 (DIAPH1)

The actin cytoskeleton is a dynamic array of filaments that undergoes rapid remodeling to drive many cellular processes. An essential feature of filament remodeling is the spatio-temporal regulation of actin filament nucleation. One family of actin filament nucleators, the Diaphanous-related formins, is activated by the binding of small G-proteins such as RhoA. However, RhoA only partially activates formins, suggesting that additional factors are required to fully activate the formin. Here we identify one such factor, IQ motif containing GTPase activating protein-1 (IQGAP1), which enhances RhoA-mediated activation of the Diaphanous-related formin (DIAPH1) and targets DIAPH1 to the plasma membrane. We find that the inhibitory intramolecular interaction within DIAPH1 is disrupted by the sequential binding of RhoA and IQGAP1. Binding of RhoA and IQGAP1 robustly stimulates DIAPH1-mediated actin filament nucleation in vitro In contrast, the actin capping protein Flightless-I, in conjunction with RhoA, only weakly stimulates DIAPH1 activity. IQGAP1, but not Flightless-I, is required to recruit DIAPH1 to the plasma membrane where actin filaments are generated. These results indicate that IQGAP1 enhances RhoA-mediated activation of DIAPH1 in vivo Collectively these data support a model where the combined action of RhoA and an enhancer ensures the spatio-temporal regulation of actin nucleation to stimulate robust and localized actin filament production in vivo.

Study of the Bacillus thuringiensis Cry1Ia Protein Oligomerization Promoted by Midgut Brush Border Membrane Vesicles of Lepidopteran and Coleopteran Insects, or Cultured Insect Cells.

Bacillus thuringiensis (Bt) produces insecticidal proteins that are either secreted during the vegetative growth phase or accumulated in the crystal inclusions (Cry proteins) in the stationary phase. Cry1I proteins share the three domain (3D) structure typical of crystal proteins but are secreted to the media early in the stationary growth phase. In the generally accepted mode of action of 3D Cry proteins (sequential binding model), the formation of an oligomer (tetramer) has been described as a major step, necessary for pore formation and subsequent toxicity. To know if this could be extended to Cry1I proteins, the formation of Cry1Ia oligomers was studied by Western blot, after the incubation of trypsin activated Cry1Ia with insect brush border membrane vesicles (BBMV) or insect cultured cells, using Cry1Ab as control. Our results showed that Cry1Ia oligomers were observed only after incubation with susceptible coleopteran BBMV, but not following incubation with susceptible lepidopteran BBMV or non-susceptible Sf21 insect cells, while Cry1Ab oligomers were persistently detected after incubation with all insect tissues tested, regardless of its host susceptibility. The data suggested oligomerization may not necessarily be a requirement for the toxicity of Cry1I proteins.

A Single Step in vitro Bioassay Mimicking TLR4-LPS Pathway and the Role of MD2 and CD14 Coreceptors.

Acute systemic Gram-negative bacterial infections are accompanied by release of lipopolysaccharide (LPS) endotoxins into the bloodstream and an innate immune host response via the well-known toll like receptor 4 (TLR4) pathway. In this, LPS associates non-covalently with TLR4 to form an activated heterodimer (LPS/MD2/TLR4)2 complex in vivo, assisted by a coreceptor CD14. This complexation process has been illustrated ex vivo using indirect methods such as cytokine, interleukin, TNF-α measurements and by direct demonstration of sequential binding events on a surface using advanced optics. We are the first ones to carry out homogeneous self-assembly of LPS-rTLR4-MD2 conjugates in vitro in a single step, and further demonstrate the role of CD14 as a catalyst during this process. The assay comprises of LPS, MD2, CD14, and recombinant TLR4-conjugated magnetic particles co-incubated in a buffer at room temperature. The complexes are removed by magnetic separation and the extent of binding is estimated by quantifying the unbound biomolecules in the supernatant using standard biophysical techniques. Our results show that rTLR4-MD2-LPS complexes form in an hour and follow a 1:1:1 stoichiometry, in agreement with the in vivo/ex vivo studies. The assay is also highly specific; addition of known LPS-binding ligands decreased the LPS-rTLR4 complexation, allowing its use as a rapid tool for molecular inhibitor screening.

Sequential Detection of Palladium and Chromium Oxyanion by a Fluorescein Based Chemosensor in Mixed Aqueous Media

A new highly selective chemosensor, based on fluorescein-allyloxy benzene conjugate 1, was developed for the sequential detection of palladium and chromium oxyanions in a mixed aqueous media, and was studied by UV-visible and fluorescence spectroscopy. The sensing of palladium ions produces a chemodosimetric and ratiometric change in the emission band of 1 from 450 to 525 nm, followed by the sensing of chromate ions by 2 that quenches the emission band at 525 nm in a buffered H2O: DMF solution (9:1, pH = 7.4). The rate constants of palladium and chromate ions were found to be 8.6 × 105 M−1, 2.1 × 105 M−1, and 5.4 × 104 M−1 respectively. The chemosensor 1 has a palladium detection limit of 49 ppb while the sequential detection limit of chromate ions (CrO42− and Cr2O72−) were 127 and 259 ppb. The ratiometric change in the emission is produced due to the deallylation of 1 by palladium to produce 2 that restores the ESIPT (excited state intramolecular proton transfer) of the phenolic ring and enhances the electron transfer (ET) phenomenon from the phenolic group to fluorescein. The sequential binding of chromate ions to 2 inhibits the ESIPT and causes chelation enhanced quenching (CHEQ) of the fluorescence.

Isothermal titration calorimetry and surface plasmon resonance analysis using the dynamic approach

Biophysical techniques such as isothermal titration calorimetry (ITC) and surface plasmon resonance (SPR) are routinely used to ascertain the global binding mechanisms of protein-protein or protein-ligand interaction. Recently, Dumas etal, have explicitly modelled the instrument response of the ligand dilution and analysed the ITC thermogram to obtain kinetic rate constants. Adopting a similar approach, we have integrated the dynamic instrument response with the binding mechanism to simulate the ITC profiles of equivalent and independent binding sites, equivalent and sequential binding sites and aggregating systems. The results were benchmarked against the standard commercial software Origin-ITC. Further, the experimental ITC chromatograms of 2′-CMP + RNASE and BH3I-1 + hBCLXL interactions were analysed and shown to be comparable with that of the conventional analysis. Dynamic approach was applied to simulate the SPR profiles of a two-state model, and could reproduce the experimental profile accurately.

BiAb Mediated Restoration of the Linkage between Dystroglycan and Laminin-211 as a Therapeutic Approach for α-Dystroglycanopathies.

Patients with α-dystroglycanopathies, a subgroup of rare congenital muscular dystrophies, present with a spectrum of clinical manifestations that includes muscular dystrophy as well as CNS and ocular abnormalities. Although patients with α-dystroglycanopathies are genetically heterogeneous, they share a common defect of aberrant post-translational glycosylation modification of the dystroglycan alpha-subunit, which renders it defective in binding to several extracellular ligands such as laminin-211 in skeletal muscles, agrin in neuromuscular junctions, neurexin in the CNS, and pikachurin in the eye, leading to various symptoms. The genetic heterogeneity associated with the development of α-dystroglycanopathies poses significant challenges to developing a generalized treatment to address the spectrum of genetic defects. Here, we propose the development of a bispecific antibody (biAb) that functions as a surrogate molecular linker to reconnect laminin-211 and the dystroglycan beta-subunit to ameliorate sarcolemmal fragility, a primary pathology in patients with α-dystroglycan-related muscular dystrophies. We show that the treatment of LARGEmyd-3J mice, an α-dystroglycanopathy model, with the biAb improved muscle function and protected muscles from exercise-induced damage. These results demonstrate the viability of a biAb that binds to laminin-211 and dystroglycan simultaneously as a potential treatment for patients with α-dystroglycanopathy.

Phosphorylation of the multifunctional signal transducer B-cell adaptor protein (BCAP) promotes recruitment of multiple SH2/SH3 proteins including GRB2

B-cell adaptor protein (BCAP) is a multimodular, multifunctional signal transducer that regulates signal transduction pathways in leukocytes, including macrophages, B-cells, and T-cells. In particular, BCAP suppresses inflammatory signaling by Toll-like receptors (TLRs). However, how BCAP itself is regulated and what its interaction partners are is unclear. Here, using human immune cell lines, including THP-1 cells, we characterized the complex phosphorylation patterns of BCAP and used a novel protein complex trapping strategy, called virotrap, to identify its interaction partners. This analysis identified known interactions of BCAP with phosphoinositide 3-kinase (PI3K) p85 subunit and NCK adaptor protein (NCK), together with previously unknown interactions of BCAP with Src homology 2 (SH2) and SH3 domain-containing adaptor proteins, notably growth factor receptor-bound protein 2 (GRB2) and CRK-like proto-oncogene, adaptor protein (CRKL). We show that the SH3 domain of GRB2 can bind to BCAP independently of BCAP phosphorylation status, suggesting that the SH2 domains mediate interactions with activated receptor tyrosine kinase complexes including the CD19 subunit of the B-cell receptor. Our results also suggested that the PI3K p85 subunit binds to BCAP via SH3 domains forming an inactive complex that is then activated by sequential binding with the SH2 domains. Taken together, our results indicate that BCAP is a complex hub that processes signals from multiple pathways in diverse cell types of the immune system.

Remote Ligand Modifications Tune Electronic Distribution and Reactivity in Site-Differentiated, High-Spin Iron Clusters: Flipping Scaling Relationships.

We report the synthesis, characterization, and reactivity of [LFe3O(RArIm)3Fe][OTf]2, the first Hammett series of a site-differentiated cluster. The cluster reduction potentials and CO stretching frequencies shift as expected on the basis of the electronic properties of the ligand: electron-donating substituents result in more reducing clusters and weaker C-O bonds. However, unusual trends in the energetics of their two sequential CO binding events with the substituent σp parameters are observed. Specifically, introduction of electron-donating substituents suppresses the first CO binding event (ΔΔH by as much as 7.9 kcal mol-1) but enhances the second (ΔΔH by as much as 1.9 kcal mol-1). X-ray crystallography, including multiple-wavelength anomalous diffraction, Mössbauer spectroscopy, and SQUID magnetometry, reveal that these substituent effects result from changes in the energetic penalty associated with electronic redistribution within the cluster, which occurs during the CO binding event.

Triple-Pnictogen Bonding as a Tool for Supramolecular Assembly.

Supramolecular assembly utilizing simultaneous formation of three pnictogen bonds around a single antimony vertex was explored via X-ray crystallography, solution NMR, and computational chemistry. An arylethynyl (AE) ligand was designed to complement the three electrophilic regions around the Sb compound. Though solution studies reveal large binding constants for individual pyridyl units with the Sb donor, the rigidity and prearrangement of the AE acceptor proved necessary to achieve simultaneous binding of three acceptors to the Sb-centered pnictogen-bond donor. Calculations and X-ray structures suggest that negative cooperativity upon sequential binding of three acceptors to a Sb center limits the utility of triple-pnictogen bonding pyridyl acceptors. These limitations can be negated, however, when positive cooperativity is designed into a complementary acceptor ligand.

Fractal-seaweeds type functionalization of graphene

Abstract In this work, we present a systematic investigation on the regioselectivity and topicity of radical hydrogenation/alkylation of graphene. The complex process of sequential covalent binding of hydrogen and methyl radicals to the edges and basal plane of graphene, and addition to the direct neighborhood of pre-existing defects were quantitatively investigated using different computational techniques. Considering both thermodynamic and kinetic factors a general model for graphene functionalization has been developed. Based on the proposed model we performed numerical Monte-Carlo simulations, which provide evidence of a fractal expansion of functionalized regions leading to a fractal-seaweeds type of addition. We show that the applications of the model is widespread and includes the description of Birch-like hydrogenation, reductive alkylation and direct radical addition, which allows to evaluate the effect of the size, shape and the quality of a graphene flake on the addition morphology.

Modeling of Multivalent Ligand-Receptor Binding Measured by kinITC

In addition to the conventional Isothermal Titration Calorimetry (ITC), kinetic ITC (kinITC) not only gains thermodynamic information, but also kinetic data from a biochemical binding process. Moreover, kinITC gives insights into reactions consisting of two separate kinetic steps, such as protein folding or sequential binding processes. The ITC method alone cannot deliver kinetic parameters, especially not for multivalent bindings. This paper describes how to solve the problem using kinITC and an invariant subspace projection. The algorithm is tested for multivalent systems with different valencies.

Efficient pre-catalytic conformational change of reverse transcriptases from SAMHD1 non-counteracting primate lentiviruses during dNTP incorporation

Unlike HIV-1, HIV-2 and some SIV strains replicate at high dNTP concentrations even in macrophages due to their accessory proteins, Vpx or Vpr, that target SAMHD1 dNTPase for proteasomal degradation. We previously reported that HIV-1 reverse transcriptase (RT) efficiently synthesizes DNA even at low dNTP concentrations because HIV-1 RT displays faster pre-steady state kpol values than SAMHD1 counteracting lentiviral RTs. Here, since the kpol step consists of two sequential sub-steps post dNTP binding, conformational change and chemistry, we investigated which of the two sub-steps RTs from SAMHD1 non-counteracting viruses accelerate in order to complete reverse transcription in the limited dNTP pools found in macrophages. Our study demonstrates that RTs of SAMHD1 non-counteracting lentiviruses have a faster conformational change rate during dNTP incorporation, supporting that these lentiviruses may have evolved to harbor RTs that can efficiently execute the conformational change step in order to circumvent SAMHD1 restriction and dNTP depletion in macrophages.

Novel Aza-BODIPY based turn on selective and sensitive probe for on-site visual detection of bivalent copper ions

3-Ethoxy-N,N-diethylaniline substituted aza-BODIPY dye (7) was designed and synthesized that could recognize Cu (II) ions through sequential binding interactions. The visible changes in the absorption and enhancement in fluorescence intensity with the addition of Cu (II) ions makes this dye as a selective and sensitive probe for on-site visual detection and analysis. The presence of 3-ethoxy-N,N-diethylaniline group at the peripheral positions shifted its absorption to the near-infrared region, ca. 640–890 nm of the electromagnetic spectrum. This dye showed a gradual shift in the absorption maximum towards red with the increase in polarity of the medium. The triplet excited state properties of this dye suggest that it shows negligible singlet oxygen generation efficiency. The dye possesses excellent photostability, low fluorescence quantum yields, sharp absorption bands in the near-infrared region (NIR) and exhibits selective interactions with Cu(II) ions. The limit of detection was found to be as low as 350 nm and selectivity was not interfered by other metal ions and anions, thereby demonstrating its use as a novel probe for the detection and analysis of copper ions through visual absorption changes and ‘turn on’ fluorescence intensity.

A cyanine dye-based fluorescent probe as indicator of copper clock reaction for tracing Cu2+-catalyzed oxidation of cysteine

Using cyanine dye-coupling 2-pyridylmethyl chelating unit as fluorescent probe, we successfully developed an indicator of copper clock reaction to monitor the process of cysteine (Cys) oxidation. During the monitoring assay, the fluorescent changes reflected three sequential reaction and binding behaviors including oxidation of Cys, oxidation of Cu(I) and binding between Cu(II) and the oxidation product cystine (Cys-Cys). Because the different kinetic trajectories were obtained when used Cys, GSH and Hcy as the substrates, respectively, a new strategy for distinguishing Cys from GSH and Hcy was further developed using the cyanine dye-coupling Cu(II) complex.

Binding to The Target Cell Surface Is The Crucial Step in Pore Formation of Hemolysin BL from Bacillus cereus.

A major virulence factor involved in Bacillus cereus food poisoning is the three-component enterotoxin hemolysin BL. It consists of the binding component B and the two lytic components L1 and L2. Studying its mode of action has been challenging, as natural culture supernatants additionally contain Nhe, the second three-component enterotoxin, and purification of recombinant (r) Hbl components has been difficult. In this study, we report on pore-forming, cytotoxic, cell binding and hemolytic activity of recently generated rHbl components expressed in E. coli. It is known that all three Hbl components are necessary for cytotoxicity and pore formation. Here we show that an excess of rHbl B enhances, while an excess of rHbl L1 hinders, the velocity of pore formation. Most rapid pore formation was observed with ratios L2:L1:B = 1:1:10 and 10:1:10. It was further verified that Hbl activity is due to sequential binding of the components B - L1 - L2. Accordingly, all bioassays proved that binding of Hbl B to the cell surface is the crucial step for pore formation and cytotoxic activity. Binding of Hbl B took place within minutes, while apposition of the following L1 and L2 occurred immediately. Further on, applying toxin components simultaneously, it seemed that Hbl L1 enhanced binding of B to the target cell surface. Overall, these data contribute significantly to the elucidation of the mode of action of Hbl, and suggest that its mechanism of pore formation differs substantially from that of Nhe, although both enterotoxin complexes are sequentially highly related.

Gold Nanoparticle-Induced Photocurrent Quenching and Recovery of Polymer Dots: Toward Signal-On Energy-Transfer-Based Photocathodic Bioanalysis of Telomerase Activity in Cell Extracts.

Energy transfer (ET) in photoelectrochemical (PEC) bioanalysis is usually generated between noble metal nanoparticles (NPs) and traditional inorganic quantum dots (QDs). Using the innovative polymer dot (Pdot)-involved ET, this work reports the first signal-on and cathodic PEC bioanalysis toward telomerase (TE) activity in cell extracts. Specifically, the sequential binding of capture DNA (cDNA), telomerase primer sequence (TS), and Au NP-labeled probe DNA (Au NP-pDNA) on the electrode would place the Au NPs in close proximity of the Pdots, leading to obvious quenching of the cathodic photocurrent. The subsequent extension of the TS by TE in the presence of deoxyribonucleoside triphosphates (dNTPs) would then release the Ag NP-pDNA from the electrode, leading to the recovery of the photocurrent. On the basis of the Au NP-induced photocurrent quenching and the recovery of Pdots, a sensitive biosensor could thus be developed by tracking the photocurrents to probe the TE activity. This strategy allows for signal-on and cathodic PEC bioanalysis of TE, which can be easily extended for numerous other targets of interest. We believe this work could offer a new perspective for the rational implementation of Pdot-involved ET for advanced PEC bioanalysis.

Aqueous Micro-hydration of Na+(H2O)n=1-7 Clusters: DFT Study

AbstractSodium ion micro-solvated clusters, [Na(H2O) n]+, n = 1–7, were completed by (DFT) density functional theory at B3LYP/6-311+G(d,p) level in the gaseous phase. At the ambient situation, the four, five and six micro-solvated configurations can convert from each other. The investigation of the sequential water binding energy on Na+ obviously indicates that the influence of Na+ on the neighboring water molecules goes beyond the first solvation layer with the hydration number of 5. The hydration number of Na+ is 5 and the hydration space (rNa-O) is 2.43 Å. The current study displays that all our simulations have an brilliant harmony with the diffraction result from X-ray scattering study. The vibration frequency of H2O solvent was also determined. This work is important for additional identification of the Na+(H2O)n clusters in aqueous medium.

PH‐Controlled Multiple Interconversion between Cucurbit[7]uril‐Based Molecular Shuttle, [3]Pseudorotaxane and [2]Pseudorotaxane

AbstractAn axle molecule 12+ containing one viologen nucleus and two identical p‐toluic acid sides was synthesized. The sequential binding of the Q[7] wheels to the 12+ axle leads to the formation of a molecular shuttle and then a homowheel, [3]pseudorotaxane. The [3]pseudorotaxane can reversibly transform to [2]pseudorotaxane by acid‐base control. On the other hand, the initially formed molecular shuttle can also transform to [2]pseudorotaxane directly and reversibly under pH control. As a whole, a molecular shuttle and [3]/[2]pseudorotaxanes constructed a pH‐controlled multiple interconvertible system.

Communication between the Ligand-Binding Pocket and the Activation Function-2 Domain of Androgen Receptor Revealed by Molecular Dynamics Simulations.

Androgen receptor (AR), as a member of the nuclear receptor (NR) superfamily, regulates the gene transcription in response to the sequential binding of diverse agonists and coactivators. Great progress has been made in studies on the pharmacology and structure of AR, but the atomic level mechanism of the bidirectional communications between the ligand-binding pocket (LBP) and the activation function-2 (AF2) region of AR remains poorly understood. Therefore, in this study, molecular dynamics (MD) simulations and free energy calculations were carried out to explore the interactions among water, agonist (DHT) or antagonist (HFT), AR, and coactivator (SRC3). Upon the binding of an agonist (DHT) or antagonist (HFT), the LBP structure would transform to the agonistic or antagonistic state, and the conformational changes of the LBP would regulate the structure of the AF2 surface. As a result, the binding of the androgen DHT could promote the recruitment of the coactivator SRC3 to the AF2, and on the contrary, the binding of the antagonist HFT would induce a perturbation to the shape of the AF2 and then weaken its accommodating capability of the coactivators with the LXXLL motif. The simulation results illustrated that the DHT-AR binding affinity was enhanced by the association of the coactivator SRC3, which would reduce the conformational fluctuation of the AR-LBD and expand the size of the AR LBP. On the other hand, the coactivator-to-HFT allosteric pathway, which involves the SRC3, helix 3 (H3), helix 4 (H4), the loop (L1-3) between helix 1 (H1) and H3, and HFT, was characterized. The HFT's skewness and different interactions between HFT and the LBP were observed in the SRC3-present AR. The mutual communications between the AF2 surface and LBP, together with the processes involving the interplay of the ligand binding and coactivator recruitment events, would help in understanding the association of coactivators and rationally develop potent drugs to inhibit the activity of AR.

Exploration of tetra-branched multiple-site SO2 capture materials.

We designed a series of tetra-branched anionic structures centered with Al for more efficient SO2 capture. By using the home-made configuration search program coupled with electronic structure calculations, we have systematically explored the large reaction space consisting of these anions, cations, and SO2 molecules. Unique insertion structures of the reaction complexes featuring a SO2 molecule inserted into a branch were found to be prevalent and sometimes to be the ground states. Cations can either enhance or compress the anion-SO2 interactions, highly depending on the anion, as they have multiple ways to interact with anions and SO2 molecules. According to the calculated sequential SO2 binding energies (with the cation effect included), [Al(Im)4]- is expected to be the best among the designed structures for reversible SO2 capture. This approach can be easily extended to design and screen sorbents for other acidic gases.