Keum Young Ahn

A highly sensitive and selective diagnostic assay based on virus nanoparticles.

Early detection of the protein marker troponin I in patients with a higher risk of acute myocardial infarction can reduce the risk of death from heart attacks. Most troponin assays are currently based on the conventional enzyme linked immunosorbent assay and have detection limits in the nano- and picomolar range. Here, we show that by combining viral nanoparticles, which are engineered to have dual affinity for troponin antibodies and nickel, with three-dimensional nanostructures including nickel nanohairs, we can detect troponin levels in human serum samples that are six to seven orders of magnitude lower than those detectable using conventional enzyme linked immunosorbent assays. The viral nanoparticle helps to orient the antibodies for maximum capture of the troponin markers. High densities of antibodies on the surfaces of the nanoparticles and nanohairs lead to greater binding of the troponin markers, which significantly enhances detection sensitivities. The nickel nanohairs are re-useable and can reproducibly differentiate healthy serum from unhealthy ones. We expect other viral nanoparticles to form similar highly sensitive diagnostic assays for a variety of other protein markers.

A novel approach to ultrasensitive diagnosis using supramolecular protein nanoparticles

We report on the ultrasensitive protein nanoprobe system that specifically captures disease marker (autoantibodies of Type I diabetes in this case) with attomolar sensitivity. The system relies on supramolecular protein nanoparticles that bind a specific antibody [65 kDa glutamate decarboxylase (GAD65)‐specific autoantibody, i.e., the early marker of Type I diabetes]. The ultrasensitive detection of early marker of Type I diabetes during the early phase of pancreatic β‐cell destruction is important because individuals at high risk of developing Type I diabetes can be identified several years before the clinical onset of the ailment. The bacterial expression of chimera genes encoding N‐[human ferritin heavy chain (hFTN‐H)]::[specific antigenic epitope]‐C produces supramolecular nanoparticles with uniform diameters (10‐15 nm), owing to self‐assembly activity of hFTN‐H. Each nanoparticle, formed by intermolecular self‐assembly between the chimera protein molecules, is subjected to carrying a large number (presumably, 24) of epitopes with a homogeneous and stable conformation per autoantibody binding, thereby allowing substantial enhancement of sensitivity. The sensitivity was finally boosted to 3 attomolar concentration of the autoantibodies, 4‐9 orders of magnitude more sensitive than conventional immunoassays. Also, this ultrasensitive protein nanoprobe successfully detected natural autoantibodies in the sera from Type I diabetic patients. The attomolar sensitivity was successfully reproduced on the detection of other antibodies, i.e., monoclonal antibodies against hepatitis B surface antigen. With the two antibody markers above, the feasibility of simultaneous and multiplexing‐mode detection was also demonstrated.—Lee S‐H., Lee, H., Park J‐S., Choi, H., Han K‐Y., Seo H‐S., Ahn K‐Y., Han S‐S., Cho, Y., Lee K‐H., Lee J. A novel approach to ultrasensitive diagnosis using supramolecular protein nano‐particles. FASEB J. 21, 1324–1334 (2007)

A Novel Bioassay Platform Using Ferritin‐Based Nanoprobe Hydrogel

Ferritin-based nanoprobe (FBNP) hydrogel was synthesized through a simple one-step copolymerization and used as a diagnostic assay platform to solve the traditional problems [ 1–6 ] (i.e., low sensitivity and specifi city, infeasibility of multiplex assays, random orientation of probes, probe instability, uncontrollable probe loading, etc.) of ELISA (enzyme-linked immunosorbent assay)-based bioassays. Here we show the advantages of the diagnostic assays based on FBNP hydrogel: probe immobilization without a random orientation problem, controllable loading of homogeneously oriented probes, protein-friendly environment, suffi cient storage stability, much higher sensitivity than ELISA, and high specifi city and reproducibility even in multiplex assays. FBNP hydrogel was successfully applied to the sensitive and specifi c diagnostic assays of acquired immune defi ciency syndrome (AIDS) [ 7–9 ] and Sjögren’s syndrome (SS). [ 10–12 ] Although the diagnostic assays of AIDS and SS were demonstrated as proof-of-concept in this study, FBNP hydrogel can be applied in general to sensitive and specifi c detection of many other disease markers. Proteins are chemically and structurally complex with a heterogeneous outer surface and they easily lose their structure and biochemical activity as a result of denaturation, dehydration, or oxidation. Therefore, in protein detection assays that are based on specifi c interactions between the protein probe and protein analyte/target/marker (e.g., antibody–antigen interaction), it is of crucial importance to design a novel assay platform that stably maintains the native conformation, analyte binding affi nity, high surface density, and stability of welloriented protein probes on the assay surface. [ 13 , 14 ] The conventional methods that use protein probes are based on attachment of probes on the reactive surface that is modifi ed either for passive adsorption or for covalent coupling of primary amine

Solubility enhancement of aggregation-prone heterologous proteins by fusion expression using stress-responsive Escherichia coli protein, RpoS.

BackgroundThe most efficient method for enhancing solubility of recombinant proteins appears to use the fusion expression partners. Although commercial fusion partners including maltose binding protein and glutathione-S-transferase have shown good performance in enhancing the solubility, they cannot be used for the proprietory production of commercially value-added proteins and likely cannot serve as universal helpers to solve all protein solubility and folding issues. Thus, novel fusion partners will continue to be developed through systematic investigations including proteome mining presented in this study.ResultsWe analyzed the Escherichia coli proteome response to the exogenous stress of guanidine hydrochloride using 2-dimensional gel electrophoresis and found that RpoS (RNA polymerase sigma factor) was significantly stress responsive. While under the stress condition the total number of soluble proteins decreased by about 7 %, but a 6-fold increase in the level of RpoS was observed, indicating that RpoS is a stress-induced protein. As an N-terminus fusion expression partner, RpoS increased significantly the solubility of many aggregation-prone heterologous proteins in E. coli cytoplasm, indicating that RpoS is a very effective solubility enhancer for the synthesis of many recombinant proteins. RpoS was also well suited for the production of a biologically active fusion mutant of Pseudomonas putida cutinase.ConclusionRpoS is highly effective as a strong solubility enhancer for aggregation-prone heterologous proteins when it is used as a fusion expression partner in an E. coli expression system. The results of these findings may, therefore, be useful in the production of other biologically active industrial enzymes, as successfully demonstrated by cutinase.

Engineered protein nanoparticles for in vivo tumor detection

Two different protein nanoparticles that are totally different in shape and surface structure, i.e. Escherichia coli DNA-binding protein (eDPS) (spherical, 10 nm) and Thermoplasma acidophilum proteasome (tPTS) (cylindrical, 12 × 15 nm) were engineered for in vivo optical tumor detection: arginine-glycine-aspartic acid (RGD) peptide (CDCRGDCFC) was genetically inserted to the surface of each protein nanoparticle, and also near-infrared fluorescence dye was chemically linked to the surface lysine residues. The specific affinity of RGD for integrin (αvβ3) facilitated the uptake of RGD-presenting protein nanoparticles by integrin-expressing tumor cells, and also the protein nanoparticles neither adversely affected cell viability nor induced cell damage. After intravenously injected to tumor-bearing mice, all the protein nanoparticles successfully reached tumor with negligible renal clearance, and then the surface RGD peptides caused more prolonged retention of protein nanoparticles in tumor and accordingly higher fluorescence intensity of tumor image. In particular, the fluorescence of tumor image was more intensive with tPTS than eDPS, which is due presumably to longer in vivo half-life and circulation of tPTS that originates from thermophilic and acidophilic bacterium. Although eDPS and tPTS were used as proof-of-concept in this study, it seems that other protein nanoparticles with different size, shape, and surface structure can be applied to effective in vivo tumor detection.

A sensitive diagnostic assay of rheumatoid arthritis using three-dimensional ZnO nanorod structure

We synthesized a three-dimensional nanorod structure of zinc oxide (ZnO) using a simple sol-gel process and systematically investigated properties of the ZnO nanorods regarding protein adsorption and effect on fluorescence emission. As compared to conventional polystyrene plate that has been widely used for strong protein adsorption, the ZnO nanorods had a superior protein adsorption capacity and significantly amplified fluorescence emission, suggesting the ZnO nanorods are attractive for fluorescence-based biomolecular detection assays. When applied to diagnostic assay of rheumatoid arthritis (RA) using cyclic citrullinated peptide (CCP) probe with a RCGRS motif that reportedly has a strong affinity for ZnO, the ZnO nanorods gave apparently high positive signals for all the RA-positive standards and patient sera, whereas upon the detection using conventional polystyrene plate, all the detection signals were relatively negligible. Moreover, the streptavidin-mediated immobilization of well oriented CCP further enhanced sensitivity, even for a 5000-times diluted patient serum. A highly sensitive detection of a very small amount of RA autoantibodies is important because individuals at high risk of developing RA can be identified several years before the clinical onset. Consequently, the fluorescence-based sensitive assay of RA was successfully performed using the three-dimensional ZnO nanorods, owing to the fluorescence amplification and protein/peptide adsorption properties and dimensionality of ZnO nanorods that in turn increases probe accessibility to anti-CCP RA autoantibodies. Although RA was assayed here for proof-of-concept, the ZnO nanorods-based assay can be applied in general to sensitive detection of a wide variety of antibody or protein targets.

Engineered Human Ferritin Nanoparticles for Direct Delivery of Tumor Antigens to Lymph Node and Cancer Immunotherapy

Efficient delivery of tumor-specific antigens (TSAs) to lymph nodes (LNs) is essential to eliciting robust immune response for cancer immunotherapy but still remains unsolved. Herein, we evaluated the direct LN-targeting performance of four different protein nanoparticles with different size, shape, and origin [Escherichia coli DNA binding protein (DPS), Thermoplasma acidophilum proteasome (PTS), hepatitis B virus capsid (HBVC), and human ferritin heavy chain (hFTN)] in live mice, using an optical fluorescence imaging system. Based on the imaging results, hFTN that shows rapid LN targeting and prolonged retention in LNs was chosen as a carrier of the model TSA [red fluorescence protein (RFP)], and the flexible surface architecture of hFTN was engineered to densely present RFPs on the hFTN surface through genetic modification of subunit protein of hFTN. The RFP-modified hFTN rapidly targeted LNs, sufficiently exposed RFPs to LN immune cells during prolonged period of retention in LNs, induced strong RFP-specific cytotoxic CD8+ T cell response, and notably inhibited RFP-expressing melanoma tumor growth in live mice. This suggests that the strategy using protein nanoparticles as both TSA-carrying scaffold and anti-cancer vaccine holds promise for clinically effective immunotherapy of cancer.

A simple one-step assay platform based on fluorescence quenching of macroporous silicon

We synthesized 3D macroporous silicon through a simple electrochemical dissolution process and systematically estimated its protein adsorption and effect on fluorescence emission. Compared with conventional 2D polystyrene plate, the macroporous silicon showed a superior protein adsorption capacity and significant fluorescence quenching effect. We developed a 3D macroporous silicon-based adenosine assay system through the following fabrication process: streptavidin molecules that have been immobilized on the surface of macroporous silicon are attached with biotin-linked and adenosine-specific DNA aptamer, followed by hybridization between the attached aptamer and fluorescent chemical (carboxytetramethylrhodamine/CTMR) that is conjugated with a short complementary DNA sequence. In the absence of adenosine, the aptamer-CTMR complexes remain closely attached to the surface of porous silicon, hence fluorescence being significantly quenched. Upon binding to adenosine, the DNA aptamer is subject to structure switching that leads to dissociation of CTMR from DNA aptamer, and consequently the CTMR fluorescence is restored, indicating a simple one-step assay of adenosine. Compared to the conventional 2D PS and ZnO nanorods-based assays, adenosine at much lower (sub-micromolar) concentration was successfully detected through the 3D macroporous silicon-based assay. The three-dimensionally and densely immobilized aptamer probes and effective fluorescence quenching on the surface of macroporous silicon enables adenosine to be detected at lower levels. Although the adenosine detection is reported here as a proof-of-concept, the developed macroporous silicon-based simple one-step assay platform can be applied in general to fluorescence quenching -based detection of many other biomolecules.

Human G-CSF synthesis using stress-responsive bacterial proteins

Abstract We previously reported that under the stress condition caused by the addition of 2-hydroxyethyl disulfide, a thiol-specific oxidant, to growing cultures of Escherichia coli BL21(DE3), a population of stress-responsive proteins [peptidyl-prolyl cis–trans isomerase B (PpiB), bacterioferritin (Bfr), putative HTH-type transcriptional regulator yjdC (YjdC), dihydrofolate reductase (FolA), chemotaxis protein cheZ (CheZ), and glutathione synthetase (GshB)] were significantly upregulated when compared with the nonstress condition. When those stress-responsive proteins were used as fusion partners for the expression of human granulocyte colony-stimulating factor (hG-CSF), the solubility of hG-CSF was dramatically enhanced in E. coli cytoplasm, whereas almost all of the directly expressed hG-CSF were aggregated to inclusion bodies. In addition, the spectra of circular dichroism measured with the purified hG-CSF were identical to that of standard hG-CSF, implying that the synthesized hG-CSF has native conformation. These results indicate that the bacterial stress-responsive proteins could be potent fusion expression partners for aggregation-prone heterologous proteins in E. coli cytoplasm.

Lyophilization and enhanced stability of fluorescent protein nanoparticles

Protein nanoparticles (PNPs) that are nanostructured biomaterials with intrinsic biological function have been widely employed as three-dimensional nanobiomaterials for sensitive bioassays, MRI contrast, semiconductor devices, template for hybrid materials, etc., and stable and long-term maintenance of PNPs seems to be of crucial importance. We evaluated the stability of PNPs and the efficacy of lyophilization for the long-term stability of PNPs, especially using green fluorescent protein nanoparticles (gFPNPs) as a model PNP. Fluorescence intensities and TEM images of gFPNPs were analyzed to monitor their functional and structural stabilities. Unlike the green fluorescent protein monomers (eGFP) that were gradually inactivated in aqueous solution, gFPNP in the same aqueous solution retained the initial fluorescence activity and spherical nanoparticle structure even for 2 weeks at 4°C. To ensure stable and long-term maintenance of gFPNPs, gFPNPs in aqueous solution were converted to the dried solid forms through lyophilization. It is notable that fluorescence activity and nanoparticle structure of gFPNPs that were lyophilized with both Tween 80 and sucrose were very stably maintained even for 10weeks at various storage temperatures (-20°C, 4°C, 25°C, and 37°C). During the period of 10weeks, the fluorescence of gFPNP was always more than 80% level of initial fluorescence at a wide range of temperature. Although this stability study was focused on gFPNPs, the developed optimal lyophilization conditions for gFPNPs can be applied in general to stable and long-term maintenance of many other PNP-derived biomaterials.