How Do Molecular Tweezers Bind to Proteins? Lessons from X-ray Crystallography.

To understand the biological relevance and mode of action of artificial protein ligands, crystal structures with their protein targets are essential. Here, we describe and investigate all known crystal structures that contain a so-called "molecular tweezer" or one of its derivatives with an attached natural ligand on the respective target protein. The aromatic ring system of these compounds is able to include lysine and arginine side chains, supported by one or two phosphate groups that are attached to the half-moon-shaped molecule. Due to their marked preference for basic amino acids and the fully reversible binding mode, molecular tweezers are able to counteract pathologic protein aggregation and are currently being developed as disease-modifying therapies against neurodegenerative diseases such as Alzheimer's and Parkinson's disease. We analyzed the corresponding crystal structures with 14-3-3 proteins in complex with mono- and diphosphate tweezers. Furthermore, we solved crystal structures of two different tweezer variants in complex with the enzyme Δ1-Pyrroline-5-carboxyl-dehydrogenase (P5CDH) and found that the tweezers are bound to a lysine and methionine side chain, respectively. The different binding modes and their implications for affinity and specificity are discussed, as well as the general problems in crystallizing protein complexes with artificial ligands.

Chiral separation of propranolol by electrokinetic chromatography using nanodiamonds and human serum albumin as a pseudo-stationary phase in river water.

Propranolol is currently considered as an emerging contaminant in water bodies. In this study, R- and S-propranolol were determined in river samples by electrokinetic chromatography (EKC) using nanodiamonds (NDs) and human serum albumin (HSA) as a pseudo-stationary phase in order to achieve enantioseparation. Previously, river samples were preconcentrated using a column filled with Amberlite® IR-120 and Dowex® 50WX8 resins. The setting up of influential factors such as temperature, voltage, pH, and HSA and NDs concentration is accurately described along this manuscript. A multivariate study and optimization was carried out to obtain the enantioseparation of propranolol (Rs = 2.91), which was reached under the following experimental conditions: voltage of 16 kV, temperature of 16°C, phosphate buffer pH 9.5, NDs of 0.20%, and HSA of 15 µmol l-1 . The recoveries of analytes under optimal conditions were higher than 98%. The limits of detection were 0.85 µg l-1 for R- and S-propranolol. The method was applied to real samples, and the obtained results in three different water sources studied were 1.02, 0.59, and 0.30 µg l-1 for the R-enantiomer and 0.99, 0.54, and 0.28 µg l-1 for the S-enantiomer. The accuracy of the proposed methodology (including bias and precision) has allowed us to propose it as a successful tool for the control of water quality.

CDC20 assists its catalytic incorporation in the mitotic checkpoint complex.

Open (O) and closed (C) topologies of HORMA-domain proteins are respectively associated with inactive and active states of fundamental cellular pathways. The HORMA protein O-MAD2 converts to C-MAD2 upon binding CDC20. This is rate limiting for assembly of the mitotic checkpoint complex (MCC), the effector of a checkpoint required for mitotic fidelity. A catalyst assembled at kinetochores accelerates MAD2:CDC20 association through a poorly understood mechanism. Using a reconstituted SAC system, we discovered that CDC20 is an impervious substrate for which access to MAD2 requires simultaneous docking on several sites of the catalytic complex. Our analysis indicates that the checkpoint catalyst is substrate assisted and promotes MCC assembly through spatially and temporally coordinated conformational changes in both MAD2 and CDC20. This may define a paradigm for other HORMA-controlled systems.

Open-tubular capillary electrochromatography for the simultaneous determination of cadmium and copper in plants.

We discuss the separation and determination of cadmium and copper in plant samples such as Triticum durum (wheat) and Helianthus annuus (sunflower) using open tubular capillary electrochromatography with indirect detection. Before performing the analysis, the samples were digested by microwave-assisted methods using HNO3 . Regarding the electrophoretic system, several experimental parameters were previously evaluated such as the capillary surface, mobile phase composition, buffer, pH, and voltage applied. The baseline resolution of the studied metals was obtained within 8 min by using a capillary immobilized with carboxylic multi-walled carbon nanotubes and a background electrolyte composed of 6 mM imidazole, pH 4.0. The applied voltage and the temperature were set at 20 kV and 25°C, respectively. Precision, detection, and quantification limits, along with linearity were investigated. The limits of detection and quantification were 2.20 and 7.40 µg/kg, for Cu2 ⁺ and 0.05 and 0.20 µg/kg in the case of Cd2 ⁺. A good linearity was achieved over a concentration working range of 7.5-100 and 0.2-25 µg/kg for Cu2 ⁺ and Cd2 ⁺ accordingly. Recovery data for validation studies were found in a range of 98.2-101.5% for both analytes.

Enantiomeric separation of ß-blockers and tryptophan using heparin as stationary and pseudostationary phases in capillary electrophoresis.

The separation methods of the enantiomers of two ß-blockers and tryptophan were studied using capillary electrochromatography with heparin covalently as well as non-covalently, bonded onto the capillary inner wall as stationary phase and electrokinetic chromatography with heparin as pseudostationary phase. In the case of heparin, used as a stationary phase, the method was unable to resolve enantiomers in both cases ß-blockers and tryptophan. On the other hand, when heparin was used as a pseudostationary phase, the resolution of the enantiomers was obtained only with 3-aminopropyltriethoxysilane which were immobilised onto the inner phase of the capillary. The results of this study let us infer that the electrostatic, hydrophobic, and steric interactions were involved in the separation mechanisms. The separation was achieved in less than 10 minutes under the optimized conditions: 30 mM phosphate buffer (pH 2.5) with the adding of 15 mg/mL of heparin at 15°C and 10 kV. The usefulness of heparin as a chiral selector both in electrokinetic chromatography using 3-aminopropyltriethoxysilane attached to the capillary was demonstrated for the first time. The developed method was powerful, sensitive, and fast, and it could be considered an important alternative to conventional methods used for chiral separation.

Identification of Noncatalytic Lysine Residues from Allosteric Circuits via Covalent Probes.

Covalent modifications of nonactive site lysine residues by small molecule probes has recently evolved into an important strategy for interrogating biological systems. Here, we report the discovery of a class of bioreactive compounds that covalently modify lysine residues in DegS, the rate limiting protease of the essential bacterial outer membrane stress response pathway. These modifications lead to an allosteric activation and allow the identification of novel residues involved in the allosteric activation circuit. These findings were validated by structural analyses via X-ray crystallography and cell-based reporter systems. We anticipate that our findings are not only relevant for a deeper understanding of the structural basis of allosteric activation in DegS and other HtrA serine proteases but also pinpoint an alternative use of covalent small molecules for probing essential biochemical mechanisms.

Structure of the MIS12 Complex and Molecular Basis of Its Interaction with CENP-C at Human Kinetochores.

Kinetochores, multisubunit protein assemblies, connect chromosomes to spindle microtubules to promote chromosome segregation. The 10-subunit KMN assembly (comprising KNL1, MIS12, and NDC80 complexes, designated KNL1C, MIS12C, and NDC80C) binds microtubules and regulates mitotic checkpoint function through NDC80C and KNL1C, respectively. MIS12C, on the other hand, connects the KMN to the chromosome-proximal domain of the kinetochore through a direct interaction with CENP-C. The structural basis for this crucial bridging function of MIS12C is unknown. Here, we report crystal structures of human MIS12C associated with a fragment of CENP-C and unveil the role of Aurora B kinase in the regulation of this interaction. The structure of MIS12:CENP-C complements previously determined high-resolution structures of functional regions of NDC80C and KNL1C and allows us to build a near-complete structural model of the KMN assembly. Our work illuminates the structural organization of essential chromosome segregation machinery that is conserved in most eukaryotes.

Silica nanoparticle-based microfluidic immunosensor with laser-induced fluorescence detection for the quantification of immunoreactive trypsin.

The purpose of this study was to develop a silica nanoparticle-based immunosensor with laser-induced fluorescence (LIF) as a detection system. The proposed device was applied to quantify the immunoreactive trypsin (IRT) in cystic fibrosis (CF) newborn screening. A new ultrasonic procedure was used to extract the IRT from blood spot samples collected on filter papers. After extraction, the IRT reacted immunologically with anti-IRT monoclonal antibodies immobilized on a microfluidic glass chip modified with 3-aminopropyl functionalized silica nanoparticles (APSN-APTES-modified glass chips). The bounded IRT was quantified by horseradish peroxidase (HRP)-conjugated anti-IRT antibody (anti-IRT-Ab) using 10-acetyl-3,7-dihydroxyphenoxazine (ADHP) as enzymatic mediator. The HRP catalyzed the oxidation of nonfluorescent ADHP to highly fluorescent resorufin, which was measured by LIF detector, using excitation lambda at 561nm and emission at 585nm. The detection limits (LODs) calculated for LIF detection and for a commercial enzyme-linked immunosorbent assay (ELISA) test kit were 0.87 and 4.2ngml(-1), respectively. The within- and between-assay variation coefficients for the LIF detection procedure were below 6.5%. The blood spot samples collected on filter papers were analyzed with the proposed method, and the results were compared with those of the reference ELISA method, demonstrating a potential usefulness for the clinical assessment of IRT during the early neonatal period.

Capillary electrochromatography and quartz crystal microbalance, valuable techniques in the study of heparin-lipoprotein interactions.

Atherosclerosis is initiated when lipoproteins bind to proteoglycans (PGs) in arterial walls. The binding is mediated by apolipoprotein apoB-100 and/or apoE, both of which have binding affinity toward heparin. We developed covalently bound heparin coatings for APTES-modified silica capillaries and SiO(2) chips and carried out capillary electrochromatography (CEC) and quartz crystal microbalance (QCM) studies on the interactions of heparin with selected peptide fragments of apoB-100 and apoE and, for CEC, also with low- and high-density lipoproteins (LDL and HDL), the latter with and without apoE. The peptides are known to mediate interactions of HDL and LDL with arterial PGs. Interactions and affinities were expressed in CEC as retention factors and reduced mobilities and in continuous flow QCM techniques as affinity constants. Both techniques showed heparin interactions to be stronger with apoB-100 peptide than with apoE peptide fragment, and they confirmed that the sulfate groups in heparin play an especially important role in interactions with apoB-100 peptide fragments. In addition, CEC confirmed the importance of sulfate groups of heparin in interactions between heparin and LDL and between heparin and apoE-containing HDL. CEC and QCM acted as excellent platforms to mimic these biologically important interactions, with small sample and reagent consumption.

Crystal structure of the predicted phospholipase LYPLAL1 reveals unexpected functional plasticity despite close relationship to acyl protein thioesterases.

Sequence homology indicates the existence of three human cytosolic acyl protein thioesterases, including APT1 that is known to depalmitoylate H- and N-Ras. One of them is the lysophospholipase-like 1 (LYPLAL1) protein that on the one hand is predicted to be closely related to APT1 but on the other hand might also function as a potential triacylglycerol lipase involved in obesity. However, its role remained unclear. The 1.7 Å crystal structure of LYPLAL1 reveals a fold very similar to APT1, as expected, but features a shape of the active site that precludes binding of long-chain substrates. Biochemical data demonstrate that LYPLAL1 exhibits neither phospholipase nor triacylglycerol lipase activity, but rather accepts short-chain substrates. Furthermore, extensive screening efforts using chemical array technique revealed a first small molecule inhibitor of LYPLAL1.

A combination of single-drop microextraction and open tubular capillary electrochromatography with carbon nanotubes as stationary phase for the determination of low concentration of illicit drugs in horse urine.

In this study we developed an interesting alternative to HPLC-mass spectrometry for the quantification of seven important drugs of abuse in racehorses. The procedure proposed in this work is a combination of single-drop microextraction (SDME) and an open tubular capillary electrochromatography (OT-CEC) using multi-wall carbon nanotubes (MWCTs) immobilized into a fused-silica capillary as a stationary phase. The SDME showed to be a powerful tool for extraction/preconcentration of the seven drugs analyzed in the study, showing an enrichment factor between 38- and 102-fold depending on the drug. We have investigated the electrophoretic features of MWCTs immobilized fused-silica capillary by covalent modification of the inner surface of the capillary. The results show a good run-to-run, day-to-day and capillary-to-capillary reproducibility of the method. Compared with the capillary zone electrophoresis (CZE), the coating of the capillary allowed the separation of the analytes with high resolution, with less band-broadening and without distortion of the baseline. The interactions between the analytes and the MWCTs resulted in an increased migration time and probably this was the reason of the front tailing effect. The results showed a good capillary efficiencies and an improved of the electrophoretic separation.

Three different approaches for the clarification of the interactions between lipoproteins and chondroitin-6-sulfate.

Two different experimental approaches were used for obtaining a comprehensive view and understanding of the interactions between apolipoprotein B-100 (ApoB-100) of low-density lipoprotein and apolipoprotein E (ApoE) of high-density lipoprotein and chondroitin-6-sulfate (C6S) of arterial proteoglycan. The techniques employed were partial filling affinity capillary electrophoresis (PF-ACE) and continuous flow quartz crystal microbalance (QCM). In addition, molecular dynamic (MD) simulations were used to provide a supportive visual insight into the interaction mechanism. A new tool for analysis of QCM-data was utilized, i.e., adsorption energy distribution calculations, which allowed a deeper understanding of the interactions, especially at different temperatures. The PF-ACE technique probed mainly the strong adsorption interactions whereas in the MD calculations short- and long-range interactions could be distinguished. Although there are differences in the techniques, a pretty good agreement was achieved between the three approaches for the interaction of 19 amino acid peptide of ApoB with C6S giving log affinity constants of 4.66 by QCM, 5.02 by PF-ACE, and 7.39 by MD, and for 15 amino acid peptide of ApoE with C6S 5.34 by QCM, 5.28 by PT-ACE, and 4.60 by MD at physiological temperature 37.0 °C.

Recent applications of carbon-based nanomaterials in analytical chemistry: critical review.

The objective of this review is to provide a broad overview of the advantages and limitations of carbon-based nanomaterials with respect to analytical chemistry. Aiming to illustrate the impact of nanomaterials on the development of novel analytical applications, developments reported in the 2005-2010 period have been included and divided into sample preparation, separation, and detection. Within each section, fullerenes, carbon nanotubes, graphene, and composite materials will be addressed specifically. Although only briefly discussed, included is a section highlighting nanomaterials with interesting catalytic properties that can be used in the design of future devices for analytical chemistry.

Analysis of nordihydroguaiaretic acid in Larrea divaricata Cav. extracts by micellar electrokinetic chromatography.

INTRODUCTION: Larrea divaricata Cav. is a common shrub used in folk medicine to treat a variety of diseases. The main product extracted from this bush is nordihydroguaiaretic acid (NDG), which is a potent antioxidant. OBJECTIVE: In this paper we propose a novel method for the quantification of NDG in different extracts of Larrea divaricata. The concentration of NDG in two different aqueous extracts (I and D) and an ethanolic extract (Eet) was analysed, in order to evaluate the safe use of the extracts for pharmacological purposes. METHODOLOGY: Micellar electrokinetic chromatography (MEKC) was performed under the following conditions: the background electrolyte used consisted of 20 mm phosphate buffer (pH 7.5), 10 mm sodium dodecyl sulphate and 10% acetonitrile. RESULTS: The limits of detection and quantitation of NDG were 4.54 × 10(-4) and 10.6 × 10(-4) mg/mL, respectively. The concentration of this acid in both aqueous extracts was within the safe levels. However, the decoction must be used carefully because the concentration of the acid was almost over the recommended limit. In the case of ethanolic extracts, the amount of NDG was above the safe concentration, which is in agreement with the solubility of the active compound in ethanol. CONCLUSIONS: The conclusions of this study demonstrate that most of these plant extracts should be used with care, especially those which are used with medicinal purposes. This is the first research on the quantification of NDG using MEKC in jarilla extracts.

Online immunoaffinity assay-CE using magnetic nanobeads for the determination of anti-Helicobacter pylori IgG in human serum.

About two-thirds of the world's population is infected with Helicobacter pylori (H. pylori). This Gram-negative bacterium is the most important etiological agent of chronic active type B gastritis and peptic ulcer diseases. Conventional methods such as gastric biopsy, ELISA and culture, require a long time for the determination of H. pylori infections. Moreover, the antibodies in human serum sample are capable to react immunologically with the purified H. pylori antigens immobilized on different kinds of support like magnetic nanobeads. In this study, we have developed an online immunoaffinity assay-CE to determine the concentration of anti-H. pylori IgG using magnetic nanobeads as a support of the immunological affinity ligands and an LIF as a detector. The separation was performed in 0.1 M glycine-HCl, pH 2, as the background electrolyte. The linear calibration curve to predict the concentration of H. pylori-specific immunoglobulin G antibodies in serum was produced within the range of 0.12-100 U/mL. The linear regression equation was i = 492.86+96.03 × C(anti-H. pylori), with the linear regression coefficient r(2) = 0.999. The LOD calculated by fluorescence detection procedure was of 0.06 U/mL. The whole assay was done in no more than 35 min and it was entirely automatized. The development of immunoaffinity assay-CE in this study demonstrates that there is a large possibility to introduce nanotechnology in several fields with significant advantages over the classic methodologies. Our proposition comprises the diagnosis and screening field.

Lack of TNFR p55 results in heightened expression of IFN-γ and IL-17 during the development of reactive arthritis.

Reactive arthritis (ReA) is a type of arthritis originating from certain gastrointestinal or genitourinary infections. In previous studies, we reported the development of progressive Yersinia enterocolitica-induced ReA in mice lacking TNFR p55; however, the mechanisms underlying this effect are still uncertain. In this study, we investigated the impact of TNFR p55 deficiency in modulating Ag-specific Th1 and Th17 responses during this arthritogenic process. We found more severe ReA in TNFRp55(-/-) mice compared with their wild-type (WT) counterparts. This effect was accompanied by increased levels of Yersinia LPS in the joints of knockout mice. Analysis of the local cytokine profile revealed greater amounts of IFN-γ and IL-17 in arthritic joints of TNFRp55(-/-) mice compared with WT mice at day 21 postinfection. Moreover, altered IL-17 and IFN-γ production was observed in mesenteric and inguinal lymph nodes of Yersinia-infected TNFRp55(-/-) mice, as well as in spleen cells obtained from infected mice and restimulated ex vivo with bacterial Ags. Increased levels of cytokine secretion were associated with a greater frequency of CD4(+)IL-17(+), CD4(+)IFN-γ(+), and IL-17(+)IFN-γ(+) cells in TNFRp55(-/-) mice compared with WT mice. Remarkably, Ab-mediated blockade of IL-17 and/or IFN-γ resulted in reduced joint histological scores in TNFRp55(-/-) mice. A mechanistic analysis revealed the involvement of p40, a common subunit of heterodimeric IL-12 and IL-23, in the generation of augmented IFN-γ and IL-17 production under TNFR p55 deficiency. Taken together, these data indicate that, in the absence of TNFR p55 signaling, Th1 and Th17 effector cells may act in concert to sustain the inflammatory response in bacterial-induced arthritogenic processes.

Determination of melatonin in wine and plant extracts by capillary electrochromatography with immobilized carboxylic multi-walled carbon nanotubes as stationary phase.

The finding of melatonin, the often called "hormone of darkness" in plants opens an interesting perspective associated to the plethora of health benefits related to the moderate consumption of red wine. In this study, the implementation of a new method for the determination of melatonin in complex food matrices by CEC with immobilized carboxylic multi-walled carbon nanotubes as stationary phase is demonstrated. The results indicated high electrochromatographic resolution, good capillary efficiencies and improved sensitivity respect to those obtained with conventional capillaries. In addition, it was demonstrated highly reproducible results between runs, days and columns. The LOD for melatonin was 0.01 ng/mL. The method was successfully applied to the determination of melatonin in red and white wine, grape skin and plant extracts of Salvia officinalis L.

Determination of beta-glucosidase activity in soils with a bioanalytical sensor modified with multiwalled carbon nanotubes.

Soil microorganisms and enzymes are the primary mediators of soil biological processes, including organic matter degradation, mineralization, and nutrient recycling. They play an important role in maintaining soil ecosystem quality and functional diversity. Moreover, enzyme activities can provide an indication of quantitative changes in soil organic matter. Beta-glucosidase (beta-Glu) activity has been found to be sensitive to soil management and has been proposed as a soil quality indicator because it provides an early indication of changes in organic matter status and its turnover. The aims of the present study were to test and use a simple and convenient procedure for the assay of beta-Glu activity in agricultural soil. The method described here is based on the enzymatic degradation of cellobiose by beta-Glu present in the soil sample and the subsequent determination of glucose produced by the enzymatic reaction using screen-printed carbon electrodes modified with multiwalled carbon nanotubes (SPCE-CNT) equipped with coimmobilized glucose oxidase and horseradish peroxidase enzymes. The potential applied to the SPCE-CNT detection was -0.15 V versus a Ag/AgCl pseudo-reference electrode. A linear calibration curve was obtained in the range 2.7-11.3 mM with a correlation coefficient. In the present study, an easy and effective SPCE-CNT-modified electrode allowed an improved amperometric response to be achieved and this is attributed to the increased surface area upon electrode modification.

Determination of the beta-glucosidase activity in different soils by pre capillary enzyme assay using capillary electrophoresis with laser-induced fluorescence detection.

Enzyme activities can provide indication for quantitative changes in soil organic matter (SOM). It is known that the activities of most enzymes increase as native SOM content reflecting larger microbial communities and stabilization of enzymes on humic materials. Beta-glucosidase (beta-Glu) activities have been frequently used as indicators of changes in quantity and quality of SOM. In this study we propose a simple and very sensitive method, which has lower limit of detection compared with classic spectrophotometric method with the aim of determinate the beta-Glu activity in soil samples using Fluorescein mono-beta-D-glucopyranoside (FMGlc) as a substrate. The fluorescein released by the enzymatic reaction was quantified by capillary electrophoresis-laser induced fluorescence (CE-LIF) method. The background electrolyte (BGE) consisted in 40 mM phosphate buffer, pH 6. The LOD and LOQ for fluorescein were 1.3 10(-7) mg mL(-1) and 6.4 10(-6) mg mL(-1), respectively. This work deals with the minimization of the mixture for the enzymatic reaction and with the optimization conditions of CE separation. To the best of our knowledge, this is the first time that an enzymatic activity was detected in soil using CE-LIF system.

Environmental monitoring of phenolic pollutants in water by cloud point extraction prior to micellar electrokinetic chromatography.

Many aromatic compounds can be found in the environment as a result of anthropogenic activities and some of them are highly toxic. The need to determine low concentrations of pollutants requires analytical methods with high sensitivity, selectivity, and resolution for application to soil, sediment, water, and other environmental samples. Complex sample preparation involving analyte isolation and enrichment is generally necessary before the final analysis. The present paper outlines a novel, simple, low-cost, and environmentally friendly method for the simultaneous determination of p-nitrophenol (PNP), p-aminophenol (PAP), and hydroquinone (HQ) by micellar electrokinetic capillary chromatography after preconcentration by cloud point extraction. Enrichment factors of 180 to 200 were achieved. The limits of detection of the analytes for the preconcentration of 50-ml sample volume were 0.10 microg L(-1) for PNP, 0.20 microg L(-1) for PAP, and 0.16 microg L(-1) for HQ. The optimized procedure was applied to the determination of phenolic pollutants in natural waters from San Luis, Argentina.