In situ live cell sensing of multiple nucleotides exploiting DNA/RNA aptamers and graphene oxide nanosheets.

Nucleotides, for example, adenosine-5'-triphosphate (ATP) and guanosine-5'-triphosphate (GTP), are primary energy resources for numerous reactions in organisms including microtubule assembly, insulin secretion, ion channel regulation, and so on. In order to advance our understanding of the production and consumption of nucleoside triphosphates, a versatile sensing platform for simultaneous visualization of ATP, GTP, adenosine derivates, and guanosine derivates in living cells has been built up in the present work based on graphene oxide nanosheets (GO-nS) and DNA/RNA aptamers. Taking advantage of the robust fluorescence quenching ability, unique adsorption for single-strand DNA/RNA probes, and efficient intracellular transport capacity of GO-nS, selective and sensitive visualization of multiple nucleoside triphosphates in living cells is successfully realized with the designed aptamer/GO-nS sensing platform. Moreover, GO-nS displays good biocompatibility to living cells and high protecting ability for DNA/RNA probes from enzymatic cleavage. These results demonstrate that the aptamers/GO-nS-based sensing platform is capable of selective, simultaneous, and in situ detection of multiple nucleotides, which hold a great potential for analyzing other biomolecules in living cells.

Aptamer/graphene oxide nanocomplex for in situ molecular probing in living cells.

Graphene has shown fascinating applications in bionanotechnology, including DNA sensing, protein assays, and drug delivery. However, exploration of graphene with intracellular monitoring and in situ molecular probing is still at an early stage. In this regard, we have designed an aptamer-carboxyfluorescein (FAM)/graphene oxide nanosheet (GO-nS) nanocomplex to investigate its ability for molecular probing in living cells. Results demonstrate that uptake of aptamer-FAM/GO-nS nanocomplex and cellular target monitoring were realized successfully. The dramatic delivery, protection, and sensing capabilities of GO-nS in living cells indicate that graphene oxide could be a robust candidate for many biological fields, such as DNA and protein analysis, gene and drug delivering, and intracellular tracking.

Automated 96-well purification of hexahistidine-tagged recombinant proteins on MagneHis Ni(2)+-particles.

Functional genomics and the application of high-throughput (HT) approaches to solve biological and medical questions are the main drivers behind the increasing need for HT parallel expression and purification of recombinant proteins. Automation is necessary to facilitate this complex multistep process. We describe, in detail, an HT-automated purification of hexahistidine-tagged recombinant proteins using MagneHis Ni-Particles and the Biomek FX robot. This procedure is universally applicable to hexa-histidine-tagged recombinant proteins with the tag positioned at either the N- or C-terminus. With minor modifications, the automated protein purification protocol presented in this chapter could be adapted to purify recombinant proteins bearing other tags than hexahistidine and/or other expression systems than E. coli.

Identification of phosphorylated butyrylcholinesterase in human plasma using immunoaffinity purification and mass spectrometry.

Paraoxon (diethyl 4-nitrophenyl phosphate) is an active metabolite of the common insecticide parathion and is acutely toxic due to the inhibition of cholinesterase (ChE) activity in the nervous systems. The inhibition of butyrylcholinesterase (BChE) activity by paraoxon is due to the formation of phosphorylated BChE adduct, and the detection of the phosphorylated BChE adduct in human plasma can serve as an exposure biomarker of organophosphate pesticides and nerve agents. In this study, we developed an immunoaffinity purification and liquid chromatography-mass spectrometry (LC-MS) strategy for identifying phosphorylated BChE in human plasma treated by paraoxon. BChE was captured by biotinylated anti-BChE polyclonal antibodies conjugated to streptavidin magnetic beads. Western blot analysis showed that the antibody was effective to recognize both native and modified BChE with high specificity. Using a purified BChE protein, we initially identified the exact phosphorylation site on the serine residue (S198) with a 108 Da modification by both MS/MS and accurately measured parent ion masses and quantified the extent of phosphorylation on S198 following paraoxon treatment to be >99.9%. Then, the phosphorylated BChE peptide in paraoxon-treated human plasma following immunoaffinity purification was successfully identified based on the accurate measured mass and retention time information initially obtained from the purified BChE protein. Thus, immunoaffinity purification combined with LC-MS represents a viable approach for the detection and quantification of phosphorylated BChE as an exposure biomarker of organophosphates and nerve agents.

Enzyme-linked immunosorbent assay for detection of organophosphorylated butyrylcholinesterase: a biomarker of exposure to organophosphate agents.

A sandwich enzyme-linked immunosorbent assay (sELISA) has been developed for detection of organophosphorylated butyrylcholinesterase (OP-BChE), a potential biomarker for human exposure to organophosphate insecticides and nerve agents. A pair of antibodies specific to OP-BChE adduct were identified through systematic screening of several anti BChE antibodies (anti-BChE) and anti-phosphoserine antibodies (anti-P(ser)) from different sources. The selected anti-BChE (set as capture antibody) antibodies recognize both phosphorylated and nonphosphorylated BChE. These antibodies can therefore be used to capture both BChE and OP-BChE from the sample matrices. The anti-P(ser) (set as detecting antibody) was used to recognize the OP moiety of OP-BChE adducts. With the combination of the selected antibody pair, several key parameters (such as the concentration of anti-BChE and anti-P(ser), and the blocking agent) were optimized to enhance the sensitivity and selectivity of the sELISA. Under the optimal conditions, the sELISA has shown a wide linear range from 0.03 nM to 30 nM, with a detection limit of 0.03 nM. Furthermore, the sELISA was successfully applied to detect OP-BChE using in vitro biological samples such as rat plasma spiked with OP-BChE with excellent adduct recovery (z>99%). These results demonstrate that this novel approach holds great promise to develop an ELISA kit and offers a simple and cost-effective tool for screening/evaluating exposure to organophosphate insecticides and nerve agents.

CdSe/ZnS quantum dots based electrochemical immunoassay for the detection of phosphorylated bovine serum albumin.

A CdSe/ZnS quantum dot (QD) based electrochemical immunoassay of phosphorylated bovine serum albumin (BSA-OP) as a protein biomarker is presented. The QDs were used as labels for amplifying electrochemical signals and were conjugated with a secondary anti-phosphoserine antibody in a heterogeneous sandwich immunoassay. In this assay, the model phosphorylated protein BSA-OP was added to the primary BSA antibody coated polystyrene microwells, and then the QD labeled anti-phosphoserine antibody was added for completing immunorecognition. Finally, the bound QD was dissolved in an acid-dissolution step and was detected by electrochemical stripping analysis. The measured current responses were proportional to the concentration of BSA-OP. Under optimal conditions, the voltammetric response was linear over the range of 0.5-500 ngmL(-1) of BSA-OP, with a detection limit of 0.5 ngmL(-1). It also shows good reproducibility with a relative standard deviation of 8.6%. This QD-based electrochemical immunoassay offers great promise for simple and cost-effective analysis of protein biomarkers.

Methods for mapping of interaction networks involving membrane proteins.

Nearly one-third of all genes in various organisms encode membrane-associated proteins that participate in numerous protein-protein interactions important to the processes of life. However, membrane protein interactions pose significant challenges due to the need to solubilize membranes without disrupting protein-protein interactions. Traditionally, analysis of isolated protein complexes by high-resolution 2D gel electrophoresis has been the main method used to obtain an overall picture of proteome constituents and interactions. However, this method is time consuming, labor intensive, detects only abundant proteins and is limited with respect to the coverage required to elucidate large interaction networks. In this review, we discuss the application of various methods to elucidate interactions involving membrane proteins. These techniques include methods for the direct isolation of single complexes or interactors as well as methods for characterization of entire subcellular and cellular interactomes.

The epsilon-isoform of PKC mediates the hypertonic activation of cation channels in confluent monolayers of rat hepatocytes.

We were interested whether PKC alpha, delta, epsilon or zeta is the isoform actually employed in the activation of hypertonicity-induced cation channels (HICCs) in primary cultures of rat hepatocytes. Quantitative SDS-page and Western-blot experiments revealed that PKC alpha, delta and epsilon were stimulated by Indolactam V (as a DAG substitute for activation of c and nPKCs) but that only PKC delta and epsilon did respond to hypertonic stress. Furthermore, chelation of intracellular Ca(++) by BAPTA-AM did not alter HICC activation in cable-analysis experiments whereas Indolactam V as well as V8 (an Indolactam derivative specific for PKC delta and epsilon) activated HICC currents under isotonic conditions. Finally, by use of Rottlerin (as an inhibitor exhibiting a slight preference for PKC delta over epsilon) PKC epsilon could be identified as the most likely isoform responsible for the activation of the HICC.

Automated purification of recombinant proteins: combining high-throughput with high yield.

Protein crystallography, mapping protein interactions, and other functional genomic approaches require purifying many different proteins, each of sufficient yield and homogeneity, for subsequent high-throughput applications. To fill this requirement efficiently, there is a need to develop robust, automated, high-throughput protein expression, and purification processes. We developed and compared two alternative workflows for automated purification of recombinant proteins based on expression of bacterial genes in Escherichia coli (E. coli). The first is a filtration separation protocol in which proteins of interest are expressed in a large volume, 800 ml of E. coli cultures, then isolated by filtration purification using Ni-NTA-Agarose (Qiagen). The second is a smaller scale magnetic separation method in which proteins of interest are expressed in a small volume, 25 ml, of E. coli cultures then isolated using a 96-well purification system with MagneHis Ni2+ Agarose (Promega). Both workflows provided comparable average yields of proteins, about 8 microg of purified protein per optical density unit of bacterial culture measured at 600 nm. We discuss advantages and limitations of these automated workflows, which can provide proteins with more than 90% purity and yields in the range of 100 microg to 45 mg per purification run, as well as strategies for optimizing these protocols.

Simple protein complex purification and identification method for high-throughput mapping of protein interaction networks.

Most current methods for purification and identification of protein complexes use endogenous expression of affinity-tagged bait, tandem affinity tag purification of protein complexes followed by specific elution of complexes from beads, and gel separation and in-gel digestion prior to mass spectrometric analysis of protein interactors. We propose a single affinity tag in vitro pull-down assay with denaturing elution, trypsin digestion in organic solvent, and LC-ESI MS/MS protein identification using SEQUEST analysis. Our method is simple and easy to scale-up and automate, making it suitable for high-throughput mapping of protein interaction networks and functional proteomics.

Binding of phlorizin to the C-terminal loop 13 of the Na(+)/glucose cotransporter does not depend on the [560-608] disulfide bond.

The disulfide bonds of the Na(+)/glucose cotransporter (SGLT1) are believed to participate in the binding of the transport inhibitor phlorizin. Here, we investigated the role of the [560-608] disulfide bond on the phlorizin-binding function of the C-terminal loop 13 of SGLT1 using 3-iodoacetamidophlorizin (3-IAP) as a probe. The reactivity of 3-IAP to the fully reduced loop 13 was competitively inhibited by phlorizin, as evident from the MALDI mass spectra. It indicates that the disulfide bond is not mandatory for phlorizin binding. CD and equilibrium unfolding studies showed that the secondary structure and conformation stability of loop 13 were not affected by removing the disulfide bond. Furthermore, we generated a series of loop 13 mutants to assess the contribution of the disulfide bond to phlorizin binding. A positive correlation between the stability and phlorizin affinity of the mutant proteins was observed, implying that the protein stability, rather than the disulfide bond, is relevant to the phlorizin-binding function of loop 13.

Crystallization of membrane proteins from media composed of connected-bilayer gels.

The use of hydrated-lipid gels in which the bilayer is an infinitely periodic (or at least continuous), three-dimensional structure offers a relatively new approach for the crystallization of membrane proteins. While excellent crystals of the Halobacterial rhodopsins have been obtained with such media, success remains poor in extending their use to other membrane proteins. Experience with crystallization of bacteriorhodopsin has led us to recognize a number of improvements that can be made in the use of such hydrated-gel media, which may now prove to be of general value for the crystallization of other membrane proteins.