Kinetic Binding Experiments Research Articles

Preparation and Utilization of a Highly Discriminative Absorbent Imprinted with Fetal Hemoglobin.

Development in hemoglobin-based oxygen carriers (HBOCs) that may be used as alternatives to donated blood requires an extensive supply of highly pure hemoglobin (Hb) preparations. Therefore, it is essential to fabricate inexpensive, stable and highly selective absorbents for Hb purification. Molecular imprinting is an attractive technology for preparing such materials for targeted molecular recognition and rapid separations. In this case study, we developed human fetal hemoglobin (HbF)-imprinted polymer beads through the fusion of surface imprinting and Pickering emulsion polymerization. HbF was firstly covalently coupled to silica nanoparticles through its surface-exposed amino groups. The particle-supported HbF molecules were subsequently employed as templates for the synthesis of molecularly imprinted polymers (MIPs) with high selectivity for Hb. After removing the silica support and HbF, the resulting MIPs underwent equilibrium and kinetic binding experiments with both adult Hb (HbA) and HbF. These surface-imprinted MIPs exhibited excellent selectivity for both HbA and HbF, facilitating the one-step isolation of recombinant Hb from crude biological samples. The saturation capacities of HbA and HbF were found to be 15.4 and 17.1 mg/g polymer, respectively. The present study opens new possibilities for designed resins for tailored protein purification, separation and analysis.

Addressing the Binding Mechanism of the Meprin and TRAF-C Homology Domain of the Speckle-Type POZ Protein Using Protein Engineering.

Protein-protein interactions play crucial roles in a wide range of biological processes, including metabolic pathways, cell cycle progression, signal transduction, and the proteasomal system. For PPIs to fulfill their biological functions, they require the specific recognition of a multitude of interacting partners. In many cases, however, protein-protein interaction domains are capable of binding different partners in the intracellular environment, but they require precise regulation of the binding events in order to exert their function properly and avoid misregulation of important molecular pathways. In this work, we focused on the MATH domain of the E3 Ligase adaptor protein SPOP in order to decipher the molecular features underlying its interaction with two different peptides that mimic its physiological partners: Puc and MacroH2A. By employing stopped-flow kinetic binding experiments, together with extensive site-directed mutagenesis, we addressed the roles of specific residues, some of which, although far from the binding site, govern these transient interactions. Our findings are compatible with a scenario in which the binding of the MATH domain with its substrate is characterized by a fine energetic network that regulates its interactions with different ligands. Results are briefly discussed in the context of previously existing work regarding the MATH domain.

Characterization of the folding and binding properties of the PTB domain of FRS2 with phosphorylated and unphosphorylated ligands

PTB (PhosphoTyrosine Binding) domains are protein domains that exert their function by binding phosphotyrosine residues on other proteins. They are commonly found in a variety of signaling proteins and are important for mediating protein-protein interactions in numerous cellular processes. PTB domains can also exhibit binding to unphosphorylated ligands, suggesting that they have additional binding specificities beyond phosphotyrosine recognition. Structural studies have reported that the PTB domain from FRS2 possesses this peculiar feature, allowing it to interact with both phosphorylated and unphosphorylated ligands, such as TrkB and FGFR1, through different topologies and orientations. In an effort to elucidate the dynamic and functional properties of these protein-protein interactions, we provide a complete characterization of the folding mechanism of the PTB domain of FRS2 and the binding process to peptides mimicking specific regions of TrkB and FGFR1. By analyzing the equilibrium and kinetics of PTB folding, we propose a mechanism implying the presence of an intermediate along the folding pathway. Kinetic binding experiments performed at different ionic strengths highlighted the electrostatic nature of the interaction with both peptides. The specific role of single amino acids in early and late events of binding was pinpointed by site-directed mutagenesis. These results are discussed in light of previous experimental works on these protein systems.

An intramolecular energetic network regulates ligand recognition in a SH2 domain.

In an effort to investigate the molecular determinants of ligand recognition of the C-terminal SH2 domain of the SHP2 protein, we conducted extensive site-directed mutagenesis and kinetic binding experiments with a peptide mimicking a specific portion of a physiological ligand (the scaffold protein Gab2). Obtained data provided an in-depth characterization of the binding reaction, allowing us to pinpoint residues topologically far from the binding pocket of the SH2 domain to have a role in the recognition and binding of the peptide. The presence of a sparse energetic network regulating the interaction with Gab2 was identified and characterized through double mutant cycle analysis, performed by challenging all the designed site-directed variants of C-SH2 with a Gab2 peptide mutated at +3 position relative to its phosphorylated tyrosine, a key residue for C-SH2 binding specificity. Results highlighted non-optimized residues involved in the energetic network regulating the binding with Gab2, which may be at the basis of the ability of this SH2 domain to interact with different partners in the intracellular environment. Moreover, a detailed analysis of kinetic and thermodynamic parameters revealed the role of the residue at +3 position on Gab2 in the early and late events of the binding reaction with the C-SH2 domain.

Targeting the Grb2 cSH3 domain: Design, synthesis and biological evaluation of the first series of modulators

Growth factor receptor bound protein 2 (Grb2) is an adaptor protein featured by a nSH3-SH2-cSH3 domains. Grb2 finely regulates important cellular pathways such as growth, proliferation and metabolism and a minor lapse of this tight control may totally change the entire pathway to the oncogenic. Indeed, Grb2 is found overexpressed in many tumours type. Consequently, Grb2 is an attractive therapeutic target for the development of new anticancer drug.Herein, we reported the synthesis and the biological evaluation of a series of Grb2 inhibitors, developed starting from a hit-compound already reported by this research unit. The newly synthesized compounds were evaluated by kinetic binding experiments, and the most promising derivatives were assayed in a short panel of cancer cells. Five of the newly synthesized derivatives proved to be able to bind the targeted protein with valuable inhibitory concentration in one-digit micromolar concentration. The most active compound of this series, derivative 12, showed an inhibitory concentration of about 6 μM for glioblastoma and ovarian cancer cells, and an IC50 of 1.67 for lung cancer cell. For derivative 12, the metabolic stability and the ROS production was also evaluated. The biological data together with the docking studies led to rationalize an early structure activity relationship.

Real-time temperature correction for magnetoresistive biosensors integrated with temperature modulator

Magnetoresistance-based biosensors utilize changes in electrical resistance upon varying magnetic fields to measure biological molecules or events involved with magnetic tags. However, electrical resistance fluctuates with temperature. To decouple unwanted temperature-dependent signals from the signal of interest, various methods have been proposed to correct signals from magnetoresistance-based biosensors. Yet, there is still a need for a temperature correction method capable of instantaneously correcting signals from all sensors in an array, as multiple biomarkers need to be detected simultaneously with a group of sensors in a central laboratory or point-of-care setting. Here we report a giant magnetoresistive biosensor system that enables real-time temperature correction for individual sensors using temperature correction coefficients obtained through a temperature sweep generated by an integrated temperature modulator. The algorithm with individual temperature correction coefficients obviously outperformed that using the average temperature correction coefficient. Further, temperature regulation did not eliminate temperature-dependent signals completely. To demonstrate that the method can be used in biomedical applications where large temperature variations are involved, binding kinetics experiments and melting curve analysis were conducted with the temperature correction method. The method successfully removed all temperature-dependent artifacts and thus produced more precise kinetic parameters and melting temperatures of DNA hybrids.

Development and Characterization of Fluorescent Probes for the G Protein-Coupled Receptor 35.

The orphan G protein-coupled receptor 35 (GPR35) is a potential target for the treatment of pain, inflammation, and metabolic diseases. Although many GPR35 agonists have been discovered, research on functional GPR35 ligands, such as fluorescent probes, is still limited. Herein, we developed a series of GPR35 fluorescent probes by conjugating a BODIPY fluorophore to DQDA, a known GPR35 agonist. All probes exhibited excellent GPR35 agonistic activity and desired spectroscopic properties, as determined by the DMR assay, bioluminescence resonance energy transfer (BRET)-based saturation, and kinetic binding experiments. Notably, compound 15 showed the highest binding potency and the weakest nonspecific BRET binding signal (K d = 3.9 nM). A BRET-based competition binding assay with 15 was also established and used to determine the binding constants and kinetics of unlabeled GPR35 ligands.

Monoamine oxidase binding not expected to significantly affect [18F]flortaucipir PET interpretation

Purpose[18F]-labeled positron emission tomography (PET) radioligands permit in vivo assessment of Alzheimer’s disease biomarkers, including aggregated neurofibrillary tau (NFT) with [18F]flortaucipir. Due to structural similarities of flortaucipir with some monoamine oxidase A (MAO-A) inhibitors, this study aimed to evaluate flortaucipir binding to MAO-A and MAO-B and any potential impact on PET interpretation.Methods[18F]Flortaucipir autoradiography was performed on frozen human brain tissue slices, and PET imaging was conducted in rats. Dissociation constants were determined by saturation binding, association and dissociation rates were measured by kinetic binding experiments, and IC50 values were determined by competition binding.ResultsUnder stringent wash conditions, specific [18F]flortaucipir binding was observed on tau NFT-rich Alzheimer’s disease tissue and not control tissue. In vivo PET experiments in rats revealed no evidence of [18F]flortaucipir binding to MAO-A; pre-treatment with MAO inhibitor pargyline did not impact uptake or wash-out of [18F]flortaucipir. [18F]Flortaucipir bound with low nanomolar affinity to human MAO-A in a microsomal preparation in vitro but with a fast dissociation rate relative to MAO-A ligand fluoroethyl-harmol, consistent with no observed in vivo binding in rats of [18F]flortaucipir to MAO-A. Direct binding of flortaucipir to human MAO-B was not detected in a microsomal preparation. A high concentration of flortaucipir (IC50 of 1.3 μM) was found to block binding of the MAO-B ligand safinamide to MAO-B on microsomes suggesting that, at micromolar concentrations, flortaucipir weakly binds to MAO-B in vitro.ConclusionThese data suggest neither MAO-A nor MAO-B binding will contribute significantly to the PET signal in cortical target areas relevant to the interpretation of [18F]flortaucipir.

Positive allosteric mechanisms of adenosine A1 receptor-mediated analgesia.

The adenosine A1 receptor (A1R) is a promising therapeutic target for non-opioid analgesic agents to treat neuropathic pain1,2. However, development of analgesic orthosteric A1R agonists has failed because of a lack of sufficient on-target selectivity as well as off-tissue adverse effects3. Here we show that [2-amino-4-(3,5-bis(trifluoromethyl)phenyl)thiophen-3-yl)(4-chlorophenyl)methanone] (MIPS521), a positive allosteric modulator of the A1R, exhibits analgesic efficacy in rats in vivo through modulation of the increased levels of endogenous adenosine that occur in the spinal cord of rats with neuropathic pain. We also report the structure of the A1R co-bound to adenosine, MIPS521 and a Gi2 heterotrimer, revealing an extrahelical lipid-detergent-facing allosteric binding pocket that involves transmembrane helixes 1, 6 and 7. Molecular dynamics simulations and ligand kinetic binding experiments support a mechanism whereby MIPS521 stabilizes the adenosine-receptor-G protein complex. This study provides proof of concept for structure-based allosteric drug design of non-opioid analgesic agents that are specific to disease contexts.

A strategy of utilizing Cu2+-mediating interaction to prepare magnetic imprinted polymers for the selective detection of celastrol in traditional Chinese medicines

In this work, a novel strategy to prepare molecularly imprinted polymers (MIPs) functionalized magnetic carbon nanotubes (MCNTs) via a facile sol-gel polymerization by adopting Cu2+-mediating interaction was presented for selective recognition of celastrol (Cel), in the traditional Chinese medicines (TCM). Firstly, template Cel, 3-aminopropyltriethoxysilane (APTES) as monomer and Cu2+ (co-monomer) were mixed to form a self-assembled pre-complex, in which Cu2+ could coordinate with Cel. Meanwhile, APTES plays a role of bridge between APTES and Cel. Secondly, carboxyl modified MCNTs as substrate was added into the pre-complex solution. After that, a multi-step sol-gel polymerization process was occurred in the presence of tetraethylorthosilicate as cross-linker and acetic acid as catalyst. Finally, MIPs layer was formed on the surface of the MCNTs (Cel-MIPs@MCNTs) after the removal of template with methanol/acetic. The morphology and structure of Cel-MIPs@MCNTs was investigated by various characterization techniques. The adsorption performance of Cel-MIPs@MCNTs to Cel was illustrated by kinetic, isothermal and selective binding experiments. The results displayed that the Cel-MIPs@MCNTs possessed fast kinetic equilibrium time (40 s), high adsorption capacity (13.35 μg mg−1), good imprinting factor of 3.41, and high magnetic responsivity (44.38 emu·g-1), which can be used as an ideal adsorbent for rapid isolation and enrichment of target analytes. A selective and sensitive method based on Cel-MIPs@MCNTs coupling with HPLC was developed for Cel determination including a wide linear range (0.15–200 μg mL−1) with correlation coefficient of 0.9998, a low limit of detection (0.05 μg mL−1). Furthermore, the applicability of Cel-MIPs@MCNTs was demonstrated to isolate and determine Cel in TCM samples with satisfactory recoveries ranged from 84.47% to 91.5% (RSD<5.35%). The results revealed that Cel-MIPs@MCNTs offer great potential as an adsorbent for selective and efficient isolation of Cel from complex TCM samples.

Structural basis for differential recognition of phosphohistidine-containing peptides by 1-pHis and 3-pHis monoclonal antibodies

In 2015, monoclonal antibodies (mAbs) that selectively recognize the 1-pHis or 3-pHis isoforms of phosphohistidine were developed by immunizing rabbits with degenerate Ala/Gly peptides containing the nonhydrolyzable phosphohistidine (pHis) analog- phosphotriazolylalanine (pTza). Here, we report structures of five rabbit mAbs bound to cognate pTza peptides: SC1-1 and SC50-3 that recognize 1-pHis, and their 3-pHis-specific counterparts, SC39-4, SC44-8, and SC56-2. These cocrystal structures provide insights into the binding modes of the pTza phosphate group that are distinct for the 1- and 3-pHis mAbs with the selectivity arising from specific contacts with the phosphate group and triazolyl ring. The mode of phosphate recognition in the 3-pHis mAbs recapitulates the Walker A motif, as present in kinases. The complementarity-determining regions (CDRs) of four of the Fabs interact with the peptide backbone rather than peptide side chains, thus conferring sequence independence, whereas SC44-8 shows a proclivity for binding a GpHAGA motif mediated by a sterically complementary CDRL3 loop. Specific hydrogen bonding with the triazolyl ring precludes recognition of pTyr and other phosphoamino acids by these mAbs. Kinetic binding experiments reveal that the affinity of pHis mAbs for pHis and pTza peptides is submicromolar. Bound pHis mAbs also shield the pHis peptides from rapid dephosphorylation. The epitope-paratope interactions illustrate how these anti-pHis antibodies are useful for a wide range of research techniques and this structural information can be utilized to improve the specificity and affinity of these antibodies toward a variety of pHis substrates to understand the role of histidine phosphorylation in healthy and diseased states.

Targeting the Interaction between the SH3 Domain of Grb2 and Gab2.

Gab2 is a scaffolding protein, overexpressed in many types of cancers, that plays a key role in the formation of signaling complexes involved in cellular proliferation, migration, and differentiation. The interaction between Gab2 and the C-terminal SH3 domain of the protein Grb2 is crucial for the activation of the proliferation-signaling pathway Ras/Erk, thus representing a potential pharmacological target. In this study, we identified, by virtual screening, seven potential inhibitor molecules that were experimentally tested through kinetic and equilibrium binding experiments. One compound showed a remarkable effect in lowering the affinity of the C-SH3 domain for Gab2. This inhibitory effect was subsequently validated in cellula by using lung cancer cell lines A549 and H1299. Our results are discussed under the light of previous works on the C-SH3:Gab2 interaction.

Abstract A26: Characterization and development of a GPC2 ADC for neuroblastoma and other cancers

Abstract Introduction: We previously identified glypican 2 (GPC2) as a MYCN-driven neuroblastoma oncoprotein that is robustly differentially expressed, including expression of a tumor specific isoform (Cancer Cell 2017). We exploited this differential expression by developing an antibody-drug conjugate (ADC; D3-GPC2-PBD) that showed potent efficacy in neuroblastoma patient-derived xenografts (PDXs)/xenografts (n=4) (AACR Annual Meeting 2018). Methods: To validate GPC2 expression, we performed GPC2-directed immunohistochemistry (IHC) on a high-risk neuroblastoma tumor microarray (n=64 tumors) and flow cytometry on 8 neuroblastoma PDXs. To determine the GPC2 epitope bound by this ADC, we performed X-ray crystallography and mutational studies. To define mechanisms of cytotoxicity, we quantified DNA damage and apoptosis, immunogenic cell death (ICD), and bystander cell killing. Finally, we performed a pan-cancer analysis for GPC2 expression using RNA sequencing, flow cytometry and IHC. Results: We confirmed GPC2 expression in most high-risk neuroblastomas by IHC (60/64 tumors) and all neuroblastoma PDXs by flow cytometry (8/8 tumors). Additionally, we found a bimodal GPC2 expression pattern in neuroblastoma PDXs (GPC2-Hi and GPC2-UltraHi populations). GPC2-UltraHi cells coexpressed increased levels of the stem cell markers CD133, CD338 and CD117 (e.g., GPC2-UltraHi cell CD133 mean increase mean fluorescent intensity [MFI]=34-fold of GPC2-Hi cells). Forced GPC2 overexpression in SY5Y neuroblastoma cells was sufficient to induce increased stem cell marker expression (e.g., SY5Y-GPC2 CD133 mean increase MFI=3.4-fold of native SY5Y cells). Next, structural studies revealed that the D3-GPC2-Fab binds to a conformational and tumor-specific core GPC2 epitope, findings validated by binding kinetics experiments with GPC2 mutants, and with flow cytometry and ADC susceptibility studies. ADC treatment induced upregulation of γH2AX, cleaved PARP1 and caspase 3, indicative of DNA damage and apoptosis. In addition, we showed translocation of calreticulin to the cell surface and HMGB1 release, consistent with ICD. ADC treatment of co-incubated GPC2-high/low expressing cells induced 10-62% more cytotoxicity than expected, consistent with potent bystander cell killing. Finally, we identified several other cancers that express GPC2 and initially focused on small-cell lung cancers (SCLCs). For SCLCs, we show that GPC2 is also transcriptionally activated by MYCN, expressed at ultrahigh levels on stem cells, is integral in tumor growth and dictates comparable ADC susceptibility. Similar studies in GPC2-expressing pediatric brain tumors are ongoing. Conclusions: Neuroblastomas robustly express GPC2, including ultrahigh levels in the stem cell compartment. The D3-GPC2-PBD ADC targets a conformational and tumor-specific GPC2 epitope and is potently efficacious against a diverse panel of GPC2-expressing cancers, supporting the clinical development of GPC2-directed ADCs. Citation Format: Kristopher R. Bosse, Swetha Raman, Samantha Buongervino, Maria Lane, Kristen Upton, Hong Cui, Benjamin Martinez, Daniel Martinez, Doncho V. Zhelev, Bruce Pawel, Dimiter S. Dimitrov, Jean-Philippe Julien, John M. Maris. Characterization and development of a GPC2 ADC for neuroblastoma and other cancers [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr A26.

Biochemical and structural insights into how amino acids regulate pyruvate kinase muscle isoform 2

Pyruvate kinase muscle isoform 2 (PKM2) is a key glycolytic enzyme involved in ATP generation and critical for cancer metabolism. PKM2 is expressed in many human cancers and is regulated by complex mechanisms that promote tumor growth and proliferation. Therefore, it is considered an attractive therapeutic target for modulating tumor metabolism. Various stimuli allosterically regulate PKM2 by cycling it between highly active and less active states. Several small molecules activate PKM2 by binding to its intersubunit interface. Serine and cysteine serve as an activator and inhibitor of PKM2, respectively, by binding to its amino acid (AA)-binding pocket, which therefore represents a potential druggable site. Despite binding similarly to PKM2, how cysteine and serine differentially regulate this enzyme remains elusive. Using kinetic analyses, fluorescence binding, X-ray crystallography, and gel filtration experiments with asparagine, aspartate, and valine as PKM2 ligands, we examined whether the differences in the side-chain polarity of these AAs trigger distinct allosteric responses in PKM2. We found that Asn (polar) and Asp (charged) activate PKM2 and that Val (hydrophobic) inhibits it. The results also indicate that both Asn and Asp can restore the activity of Val-inhibited PKM2. AA-bound crystal structures of PKM2 displayed distinctive interactions within the binding pocket, causing unique allosteric effects in the enzyme. These structure-function analyses of AA-mediated PKM2 regulation shed light on the chemical requirements in the development of mechanism-based small-molecule modulators targeting the AA-binding pocket of PKM2 and provide broader insights into the regulatory mechanisms of complex allosteric enzymes.

Preparation of Chitosan Molecularly Imprinted Polymers and the Recognition Mechanism for Adsorption of Alpha-Lipoic Acid.

Two effective molecularly imprinted polymers for the adsorption of alpha-lipoic acid (ALA) were synthesized by the cross-linking of chitosan with epichlorohydrin (ECH) and glutaraldehyde (GLU), respectively, in the presence of ALA as template molecules. Investigations on the molar ratios of ALA and chitosan (–NH2) in the preparation of chitosan molecularly imprinted polymers (MIPs) were carried out with a factor of ALA rebinding capabilities. The surface morphology and chemical properties of the polymers were characterized. The optimized MIPs crosslinked by ECH (MIPs–ECH) and MIPs crosslinked by GLU (MIPs–GLU) had adsorption capabilities of 12.09 mg/g and 19.72 mg/g for ALA, respectively. The adsorption behaviors of two kinds of chitosan MIPs including adsorption kinetics and isotherms were investigated in detail. Adsorption and kinetic binding experiments showed that the prepared MIPs–ECH and MIPs–GLU had selective adsorption and excellent affinity for ALA. In addition, the possible binding models between ALA and chitosan oligosaccharide were predicted by molecular dynamics simulation.

Considerations for improved performance of competition association assays analysed with the Motulsky-Mahan's "kinetics of competitive binding" model.

Background and PurposeTarget engagement dynamics can influence drugs' pharmacological effects. Kinetic parameters for drug:target interactions are often quantified by evaluating competition association experiments—measuring simultaneous protein binding of labelled tracers and unlabelled test compounds over time—with Motulsky–Mahan's “kinetics of competitive binding” model. Despite recent technical improvements, the current assay formats impose practical limitations to this approach. This study aims at the characterisation, understanding and prevention of these experimental constraints, and associated analytical challenges.Experimental ApproachMonte Carlo simulations were used to run virtual kinetic and equilibrium tracer binding and competition experiments in both normal and perturbed assay conditions. Data were fitted to standard equations derived from the mass action law (including Motulsky–Mahan's) and to extended versions aiming to cope with frequently observed deviations of the canonical traces. Results were compared to assess the precision and accuracy of these models and identify experimental factors influencing their performance.Key ResultsKey factors influencing the precision and accuracy of the Motulsky–Mahan model are the interplay between compound dissociation rates, measurement time and interval frequency, tracer concentration and binding kinetics and the relative abundance of equilibrium complexes in vehicle controls. Experimental results produced recommendations for better design of tracer characterisation experiments and new strategies to deal with systematic signal decay.Conclusions and ImplicationsOur data advances our comprehension of the Motulsky–Mahan kinetics of competitive binding models and provides experimental design recommendations, data analysis tools, and general guidelines for its practical application to in vitro pharmacology and drug screening.

Evaluation of reliability and performance of hepatitis B virus-e-antigen assays in tertiary care setting

ABSTRACTHepatitis B virus-e-antigen (HBeAg) is a viral marker to assess hepatitis B virus (HBV) replication. We have evaluated the reliability of three commonly available HBeAg immunoassays using World Health Organization-International Standard and clinical samples. In addition the performance of enzyme immunoassays (EIAs) was assessed by kinetic binding and reagent exchange experiments. Analytical and diagnostic sensitivity were significantly different among HBeAg assays (P < 0.01). The affinity of capture/detector antibodies varied significantly between EIAs (P < 0.01). Our findings suggest that significant difference in the affinity of capture/detector antibodies to HBeAg may impact the overall performance and the reliability of currently available HBeAg assays in HBV diagnosis and management.

Modification of mesoporous silica with molecular imprinting technology: A facile strategy for achieving rapid and specific adsorption

In order to improve the diffusion kinetics of molecularly imprinted materials (MIMs), applying imprinting technology to mesoporous materials is a promising strategy. In the present study, an imprinting approach based on the combination of mesoporous silica materials and molecular imprinting technology is reported. Molecularly imprinted material (MIM) for 2,4-dichlorophenoxyacetic acid (2,4-D) was prepared by using 2,4-D as the template molecule, alkyne-modified β-cyclodextrin and propargyl amine as the combinatorial functional monomers and SBA-15 as the supporter. The functional monomers were anchored to the azide-modified SBA-15 by azide–alkyne Click reaction. The synthesized MIM was characterized by transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FT-IR), elemental analysis (EA), thermal gravimetric analysis (TGA), low-angle X-ray diffraction (XRD) and N2 adsorption–desorption analysis. The interactions between template and functional monomers were studied by proton NMR analysis and UV–vis experiments. The results of the equilibrium binding experiments and selective tests showed that the prepared MIM has binding affinity and specificity for a group of analytes which have similar size and shape to those of template. Binding kinetic experiments demonstrated that the present imprinting approach can effectively enhance the mass transfer rate. The solid phase extraction of 2,4-D using MIM as the adsorbent was investigated. The extraction conditions for the processes of loading, washing and eluting were optimized. The recoveries of the molecularly imprinted solid phase extraction (MISPE) column for 2,4-D were 76.3–88.9% with relative standard deviations (RSD) of 3.48–7.64%.

The Mechanism of Acetyl Transfer Catalyzed by Mycobacterium tuberculosis GlmU.

The biosynthetic pathway of peptidoglycan is essential for Mycobacterium tuberculosis. We report here the acetyltransferase substrate specificity and catalytic mechanism of the bifunctional N-acetyltransferase/uridylyltransferase from M. tuberculosis (GlmU). This enzyme is responsible for the final two steps of the synthesis of UDP-N-acetylglucosamine, which is an essential precursor of peptidoglycan, from glucosamine 1-phosphate, acetyl-coenzyme A, and uridine 5′-triphosphate. GlmU utilizes ternary complex formation to transfer an acetyl from acetyl-coenzyme A to glucosamine 1-phosphate to form N-acetylglucosamine 1-phosphate. Steady-state kinetic studies and equilibrium binding experiments indicate that GlmU follows a steady-state ordered kinetic mechanism, with acetyl-coenzyme A binding first, which triggers a conformational change in GlmU, followed by glucosamine 1-phosphate binding. Coenzyme A is the last product to dissociate. Chemistry is partially rate-limiting as indicated by pH–rate studies and solvent kinetic isotope effects. A novel crystal structure of a mimic of the Michaelis complex, with glucose 1-phosphate and acetyl-coenzyme A, helps us to propose the residues involved in deprotonation of glucosamine 1-phosphate and the loop movement that likely generates the active site required for glucosamine 1-phosphate to bind. Together, these results pave the way for the rational discovery of improved inhibitors against M. tuberculosis GlmU, some of which might become candidates for antibiotic discovery programs.

RelA-Containing NFκB Dimers Have Strikingly Different DNA-Binding Cavities in the Absence of DNA

The main nuclear factor kappa B transcription factor family members RelA–p50 heterodimer and RelA homodimer have different biological functions and show different transcriptional activation profiles. To investigate whether the two family members adopt a similar conformation in their free states, we performed hydrogen–deuterium exchange mass spectrometry, all-atom molecular dynamics simulations, and stopped-flow binding kinetics experiments. Surprisingly, the N-terminal DNA-binding domains adopt an open conformation in RelA–p50 but a closed conformation in RelA homodimer. Both hydrogen–deuterium exchange mass spectrometry and molecular dynamics simulations indicate the formation of an interface between the N-terminal DNA-binding domains only in the RelA homodimer. Such an interface would be expected to impede DNA binding, and stopped-flow binding kinetics show that association of DNA is slower for the homodimer as compared to the heterodimer. Our results show that the DNA-binding cavity in the RelA–p50 heterodimer is open for DNA binding, whereas in the RelA homodimer, it is occluded.