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PubMedDate not supplied

Strategy for allosteric analysis based on protein-patterned stationary phase in microfluidic chip.

An effective method is presented for the on-chip analysis of chiral interactions with a successful depression of nonspecific adsorption. The alumina gel-derived protein network on poly(methyl methacrylate) (PMMA) microchannel was explored to form a protein-stationary phase and then used to carry out electrophoresis for fast enantioseparation coupled with electrochemical detection. On the basis of the chemical modification of a synthesized copolymer containing silane-functionalized scaffold, alumina sol-gel could react readily with the silane groups and form steady microstructure on the chip surface achieving the encapsulation of functional biomolecules. Compared with the native PMMA microchannels, the modified surfaces exhibited much better wettability, more stable and enhanced electroosmotic mobility, and less nonspecific adsorption. The water contact angle and EOF of alumina-gel-derived PMMA substrate were 22 degrees and 4.3 x 10(-4) cm(2) V(-1) s(-1), compared to those of 73 degrees and 1.9 x 10(-4) cm(2) V(-1) s(-1) from the untreated one, respectively. Bovine serum albumin, acting as a target protein, could be stably and homogeneously immobilized in the modified PMMA microchannel to fabricate a protein-stationary phase. Under a mild condition, D- and L-tryptophan were efficiently separated with a resolution of 1.57. The as-prepared microchip can perform chiral separations within short time, indicating that the general protocol has the potential to provide a platform for high throughput screening of enantiomer candidates such as those biochemical drugs with protein targets and the research of receptor interactions.

Adsorption↗

PubMed2004

Insulin signaling pathways in cortical dysplasia and TSC-tubers: tissue microarray analysis.

To evaluate the possible roles of the Akt/PKB-mTOR-p70S6K-S6 and cap-dependent translation (eIF4G) pathways in the pathogenesis of tuberous sclerosis complex (TSC)-associated cortical tubers and focal cortical dysplasia (FCD), we performed qualitative and semiquantitative immunohistochemical evaluation on surgically resected corticectomy specimens to detect phosphorylated molecules as activated downstream targets of the signaling pathways. A tissue microarray paraffin block was constructed from 63 archival specimens of surgically resected TSC tubers, FCDs with balloon cells, cortical dysplasia without balloon cells, and histologically normal-appearing neocortex obtained from cases with Rasmussen encephalitis, cystic-gliotic encephalopathy, and temporal lobe epilepsy. Abnormal neuroglial cells were positive for phospho-S6 and phospho-eIF4G with various staining intensities in FCDs and TSC tubers. Both proteins were much less abundantly expressed in normal-appearing neocortex. Phospho-mTOR expression was observed in neurons in all groups. The expression of phospho-S6 and phospho-eIF4G was associated with dysplastic lesions (p < 0.05), and the cytoplasmic phospho-p70S6K expression was most specific for and abundant in TSC tubers and much less prominent in other groups (p < 0.01). These results suggest that constitutive activation of cytoplasmic p70S6K plays a pivotal role in the pathogenesis of TSC tubers and that FCDs possess a distinct mechanism for activation of S6 and eIF4G.

Adolescent↗

PubMed2003

Proteomic analysis of human bronchoalveolar lavage fluid: expression profiling of surfactant-associated protein A isomers derived from human pulmonary alveolar proteinosis using immunoaffinity detection.

Human bronchoalveolar lavage fluid (BALF) proteins from pulmonary alveolar proteinosis (PAP) obtained by washing the epithelial lining of the lung with phosphate-buffered saline, were separated using high resolution two-dimensional gel electrophoresis (2-DE) under denaturing and reducing conditions. By Western blotting, the proteins were transferred from polyacrylamide gel onto a chemical resilient membrane. The surfactant-associated protein A (SP-A) isomers were then identified with enhanced chemiluminescence detection (ECL) using antibody-antigen reaction. Some of the gels were treated with silver staining after 2-DE. The molecular masses of SP-A isomers in BALF from PAP ranged from 20.5 to 26, 26 to 32, and 32 to 42 kDa, respectively; and isoelectric points (pI) were in pH range of 4.5-5.4 under denaturing and reducing conditions. In the mass range of 20.5-26 kDa and pI of 4.5-5.4, there were five isomers, and in mass range of 26-32 kDa and pI of 4.5 to 5.4, there were at least eight isomers on the ECL detection film. However, in the mass range of 32-42 kDa and pI of 4.5-5.4, there were three isomers separated one from another but there was also a cluster of overlapping spots on the ECL detection film. Thus, this communication describes a characteristic 2-DE pattern of SP-A isomers in BALF from PAP as follows. (1) The five isomers of mass 20.5-26 kDa and pI of 4.5-5.4; (2) the eight isomers of mass 26-32 kDa and pI of 4.5-5.4; and (3) the three isomers of mass 32-42 kDa and pI of 4.5-5.4.

Affinity Labels↗

PubMed2006

Identification of protein biomarkers for schizophrenia and bipolar disorder in the postmortem prefrontal cortex using SELDI-TOF-MS ProteinChip profiling combined with MALDI-TOF-PSD-MS analysis.

This paper describes the high-throughput proteomic analysis of the dorsolateral prefrontal cortex (DLPFC) from schizophrenia (SCHIZ), bipolar (BD), and normal control cohorts from the Harvard Brain Tissue Resource Center performed using ProteinChip technology based on the surface-enhanced laser desorption/ionization time of flight mass spectrometry (SELDI-TOF-MS). The resultant profiles were utilized in classification-tree algorithms for selection of protein biomarker peaks contributing maximally to the differentiation between the examined diagnostic cohorts. Twenty-four such protein biomarker peaks were identified. All of them had lower levels in the SCHIZ cohort as compared to the BD cohort. Also, 21 of these peaks were down-regulated in the SCHIZ cohort vs. the control cohort, and 7 peaks were up-regulated in the BD cohort vs. the control cohort. The proteins constituting these biomarker peaks were recognized via matrix-assisted laser desorption time of flight/postsource decay mass spectrometry (MALDI-TOF-PSD-MS). These proteins represent a wide range of functional groups involved in cell metabolism, signaling cascades, regulation of gene transcription, protein and RNA chaperoning, and other aspects of cellular homeostasis. Finally, after statistical evaluation suggesting that the selected protein biomarkers are not significantly impacted by epidemiological/tissue storage parameters (although, influence of antipsychotic and mood stabilizing drugs could not be fully excluded), the ProteinChip-based profiling was engaged again to demonstrate that the detected SCHIZ-associated changes in the levels of our protein biomarkers could also be seen in DLPFC samples from the brain collection of the Mount Sinai Medical School/Bronx Veteran Affairs Medical Center. This study demonstrates the usefulness of ProteinChip-based SELDI-TOF protein profiling in gaining insight into the molecular pathology of SCHIZ and BD as it points to changes in protein levels characterizing these diseases.

Aged↗

PubMed2005

An emerging role for comprehensive proteome analysis in human pregnancy research.

Elucidation of underlying cellular and molecular mechanisms is pivotal to the comprehension of biological systems. The successful progression of processes such as pregnancy and parturition depends on the complex interactions between numerous biological molecules especially within the uterine microenvironment. The tissue- and stage-specific expression of these bio-molecules is intricately linked to and modulated by several endogenous and exogenous factors. Malfunctions may manifest as pregnancy disorders such as preterm labour, pre-eclampsia and fetal growth restriction that are major contributors to maternal and perinatal morbidity and mortality. Despite the immense amount of information available, our understanding of several aspects of these physiological processes remains incomplete. This translates into significant difficulties in the timely diagnosis and effective treatment of pregnancy-related complications. However, the emergence of powerful mass spectrometry-based proteomic techniques capable of identifying and characterizing multiple proteins simultaneously has added a new dimension to the field of biomedical research. Application of these high throughput methodologies with more conventional techniques in pregnancy-related research has begun to provide a novel perspective on the biochemical blueprint of pregnancy and its related disorders. Further, by enabling the identification of proteins specific to a disease process, proteomics is likely to contribute, not only to the comprehension of the underlying pathophysiologies, but also to the clinical diagnosis of multifactorial pregnancy disorders. Although the application of this technology to pregnancy research is in its infancy, characterization of the cellular proteome, unearthing of functional networks and the identification of disease biomarkers can be expected to significantly improve maternal healthcare in the future.

Female↗

PubMed2006

Peptide microarray analysis of substrate specificity of the transmembrane Ser/Thr kinase KPI-2 reveals reactivity with cystic fibrosis transmembrane conductance regulator and phosphorylase.

Human lemur (Lmr) kinases are predicted to be Tyr kinases based on sequences and are related to neurotrophin receptor Trk kinases. This study used homogeneous recombinant KPI-2 (Lmr2, LMTK2, Cprk, brain-enriched protein kinase) kinase domain and a library of 1,154 peptides on a microarray to analyze substrate specificity. We found that KPI-2 is strictly a Ser/Thr kinase that reacts with Ser either preceded by or followed by Pro residues but unlike other Pro-directed kinases does not strictly require an adjacent Pro residue. The most reactive peptide in the library corresponds to Ser-737 of cystic fibrosis transmembrane conductance regulator, and the recombinant R domain of cystic fibrosis transmembrane conductance regulator was a preferred substrate. Furthermore the KPI-2 kinase phosphorylated peptides corresponding to the single site in phosphorylase and purified phosphorylase b, making this only the second known phosphorylase b kinase. Phosphorylase was used as a specific substrate to show that KPI-2 is inhibited in living cells by addition of nerve growth factor or serum. The results demonstrate the utility of the peptide library to probe specificity and discover kinase substrates and offer a specific assay that reveals hormonal regulation of the activity of this unusual transmembrane kinase.

Amino Acid Sequence↗

PubMed2005

Clinically related protein-peptide interactions monitored in real time on novel peptide chips by surface plasmon resonance imaging.

BACKGROUND: Developing rapid, high-throughput assays for detecting and characterizing protein-protein interactions is a great challenge in the postgenomic era. We have developed a new method that allows parallel analysis of multiple analytes in biological fluids and is suitable for biological and medical studies. METHODS: This technology for studying peptide-antibody interactions is based on polypyrrole-peptide chips and surface plasmon resonance imaging (SPRi). We generated a chip bearing a large panel of peptide probes by successive electro-directed copolymerizations of pyrrole-peptide conjugates on a gold surface. RESULTS: We provide evidence that (a) the signal produced by antibody binding is highly specific; (b) the detected signal specifically reflects the antibody concentration of the tested solution in a dose-dependent manner; (c) this technique is appropriate for analyzing complex media such as undiluted sera, a novelty with respect to previous techniques; and (d) correlation between classic ELISA results and the SPRi signal is good (P = 0.008). We also validated this system in a medical model by detecting anti-hepatitis C antibodies in patient-derived sera. CONCLUSION: Because of its characteristics (easy preparation of the peptide chip; high-throughput, label-free, real-time detection; high specificity; and low background), this technology is suitable for screening biological samples and for large-scale studies.

Binding Sites, Antibody↗

PubMed2006

Cytosolic heat shock proteins and heme oxygenase-1 are preferentially induced in response to specific and localized intramitochondrial damage by tetrafluoroethylcysteine.

Previously, S-(1,1,2,2-tetrafluoroethyl)-l-cysteine (TFEC) was shown to mediate cytotoxicity by covalently modifying a well-defined group of intramitochondrial proteins including aconitase, alpha-ketoglutarate dehydrogenase (alphaKGDH) subunits, heat shock protein 60 (HSP60) and mitochondrial HSP70 (mtHSP70). To investigate the cellular responses to this mitochondrial damage, microarray analysis of TFEC treated murine hepatocytes of the TAMH cell line was carried out. Results of these studies revealed a HSP response that was significantly stronger than other well-characterized hepatotoxicants including acetaminophen, diquat and rotenone. Specifically, cytosolic HSP25, HSP40, HSP70, HSP105 and microsomal HSP32 (HO-1) were strongly upregulated within the first few hours of TFEC treatment, while little change was observed among other HSPs that are predominantly localized in the mitochondria and endoplasmic reticulum (ER). Post-translational modification of HSP25 was also observed with the appearance of a unique DTT-resistant immunoreactive band at about 50kDa, a putative dimer. The biological significance of HSP responses to TFEC-induced toxicity were subsequently demonstrated using the "gain of function" pretreatment: heat shock. Overall, we report an atypical HSP induction profile that does not conform to changes expected of a classical temperature shock. Furthermore, despite a well-defined intramitochondrial origin of toxicity, TFEC rapidly evokes an early and strong upregulation of cytosolic stress proteins. The cytoprotective effects of such HSP responses suggest a plausible role in modulating the progression of TFEC-induced cellular injury.

Cell Line↗

PubMed2005

Mass spectrometric analysis of affinity-captured proteins on a dendrimer-based immunosensing surface: investigation of on-chip proteolytic digestion.

The monolayer of fourth-generation poly(amidoamine) dendrimers was adopted to construct the immunoaffinity surface of an antibody layer. The antibody layer as a bait on the dendrimer monolayer was found to result in high binding capacity of antigenic proteins and a reliable detection. The affinity-captured protein at the immunosensing surface was subjected to direct on-chip tryptic digestion, and the resulting proteolytic peptides were analyzed by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The performance of the on-chip digestion procedure was investigated with respect to the ratio of trypsin to protein, digestion time, composition of a reaction buffer, and the amount of affinity-captured protein on a surface. Addition of a water-miscible organic solvent to a reaction buffer had no significant effect on the digestion efficiency under the optimized digestion conditions. The on-chip digestion method identified the affinity-captured bovine serum albumin (BSA), lysozyme, and ferritin at the level of around 100 fmol. Interestingly, the detected number of peptide hits through the on-chip digestion was almost similar regardless of the amount of captured protein ranging from low- to high-femtomole levels, whereas the efficiency of in-solution digestion decreased significantly as the amount of protein decreased to low-femtomole levels. The structural alignment of the peptide fragments from on-chip-digested BSA revealed that the limited exterior of the captured protein is subjected to attack by trypsin. The established detection procedures enabled the identification of BSA in the biological mixtures at the level of 0.1 ng/mL. The use of antibodies against the proteins involved in the metabolic pathway of L-threonine in Escherichia coli also led to discrimination of the respective target proteins from cell lysates.

Amino Acid Sequence↗

PubMed2006

Differential profiling analysis of proteins involved in anti-proliferative effect of interferon-alpha on renal cell carcinoma cell lines by protein biochip technology.

Interferon-alpha (IFN) is widely used for the treatment of progressive renal cell carcinoma (RCC), but its effective response rate is only about 15%. New biomarkers of RCC contributing to the effective IFN treatment are needed to establish a sensitivity test for evaluating if the IFN is effective or not against RCC. All the proteins expressed in the IFN-susceptible and -resistant RCC cell lysates were analyzed by surface enhanced laser desorption ionization (SELDI) mass spectrometry using ProteinChip technology and their different protein expression were detected by the comparison of the profiles between them. We detected the following candidate markers that exhibited peak shifts: a) in the IFN-susceptible cell lines, a candidate marker with a molecular weight of 5,688 Da was detected on a hydrophobic (H4) chip: b) in the IFN-resistant cell lines, candidate markers each with a molecular weight of 8,049, 3,157, 3,993, and 8,959 Da were detected on strong anion exchange (SAX2, pH 9.0, two types) chips, H4 chip, and weak cation exchange (WCX, pH 9.0) chips, respectively. IFN treatment produced no weight increase in these four proteins, and c) candidate marker with a molecular weight of 1,623 Da that was expressed in both cell lines after the IFN treatment was detected on the H4 chip. These data suggest that the ProteinChip system is very useful in identifying proteins showing unique peaks in the RCC cell lines with different IFN susceptibility, and the comparison of these proteins measured in RCC cell lysates may help to identify the IFN sensitivity. Furthermore, the discovery of a susceptibility and or a inhibitory factor may eventually lead to the development of a novel drug targeting the respective factor for the improvement of anticancer chemotherapy.

Antineoplastic Agents↗

PubMed2004

Saccharomyces cerevisiae glutaredoxin 5-deficient cells subjected to continuous oxidizing conditions are affected in the expression of specific sets of genes.

The Saccharomyces cerevisiae GRX5 gene codes for a mitochondrial glutaredoxin involved in the synthesis of iron/sulfur clusters. Its absence prevents respiratory growth and causes the accumulation of iron inside cells and constitutive oxidation of proteins. Null Deltagrx5 mutants were used as an example of continuously oxidized cells, as opposed to situations in which oxidative stress is instantaneously caused by addition of external oxidants. Whole transcriptome analysis was carried out in the mutant cells. The set of genes whose expression was affected by the absence of Grx5 does not significantly overlap with the set of genes affected in respiratory petite mutants. Many Aft1-dependent genes involved in iron utilization that are up-regulated in a frataxin mutant were also up-regulated in the absence of Grx5. BIO5 is another Aft1-dependent gene induced both upon iron deprivation and in Deltagrx5 cells; this links iron and biotin metabolism. Other genes are specifically affected under the oxidative conditions generated by the grx5 mutation. One of these is MLP1, which codes for a homologue of the Slt2 kinase. Cells lacking MLP1 and GRX5 are hypersensitive to oxidative stress caused by external agents and exhibit increased protein oxidation in relation to single mutants. This in turn points to a role for Mlp1 in protection against oxidative stress. The genes of the Hap4 regulon, which are involved in respiratory metabolism, are down-regulated in Deltagrx5 cells. This effect is suppressed by HAP4 overexpression. Inhibition of respiratory metabolism during continuous moderately oxidative conditions could be a protective response by the cell.

Blotting, Northern↗

PubMed2004

Kinetic analysis of site-specific photoaptamer-protein cross-linking.

ssDNA oligonucleotides containing bromodeoxyuridine, BrdU-photoaptamers, are rapidly emerging as specific protein capture reagents in protein microarray technologies. A mathematical model for the kinetic analysis of photoaptamer-protein photocross-linking reactions is presented. The model is based on specific aptamer/protein binding followed by laser excitation that can lead to either covalent cross-linking of the photoaptamer and protein in the complex or irreversible photodamage to the aptamer. Two distinct kinetic regimes, (1) frozen and (2) rapid equilibrium, are developed analytically to model binding kinetics between laser pulses. The models are used to characterize the photocross-linking between three photoaptamers and their cognate protein targets; photoaptamers 0650 and 0615 cross-link human basic fibroblast growth factor and 0518 cross-links HIV MN envelope glycoprotein. Data for cross-linking reaction yields as a function of both laser energy dose and target protein concentration are analyzed for affinity constants and cross-link reaction rates. The binding dissociation constants derived from the cross-linking data are in good accord with independent measurements; the rapid equilibrium model appears to produce results more consistent with the experimental observations, although there is significant overlap between the two models for most conditions explored here. The rate of photodamage for 0615 and 0518 is 3.5 and 2.5 times that of the specific cross-link, giving low maximum reaction yields of approximately 20% and approximately 30%, whereas 0650 cross-links with a rate over five times higher than its photodamage rate and has a maximum reaction yield exceeding 80%. Quantum yields for the three systems are estimated from the data; photoaptamer 0650 has a reasonably high quantum yield of approximately 0.2 for protein cross-linking, while 0518 and 0615 have quantum yields of 0.07 and 0.02. The work presented here provides a useful set of metrics that allow for refinement of photoaptamer properties.

Binding Sites↗

PubMed2005

Single-nucleosome mapping of histone modifications in S. cerevisiae.

Covalent modification of histone proteins plays a role in virtually every process on eukaryotic DNA, from transcription to DNA repair. Many different residues can be covalently modified, and it has been suggested that these modifications occur in a great number of independent, meaningful combinations. Published low-resolution microarray studies on the combinatorial complexity of histone modification patterns suffer from confounding effects caused by the averaging of modification levels over multiple nucleosomes. To overcome this problem, we used a high-resolution tiled microarray with single-nucleosome resolution to investigate the occurrence of combinations of 12 histone modifications on thousands of nucleosomes in actively growing S. cerevisiae. We found that histone modifications do not occur independently; there are roughly two groups of co-occurring modifications. One group of lysine acetylations shows a sharply defined domain of two hypo-acetylated nucleosomes, adjacent to the transcriptional start site, whose occurrence does not correlate with transcription levels. The other group consists of modifications occurring in gradients through the coding regions of genes in a pattern associated with transcription. We found no evidence for a deterministic code of many discrete states, but instead we saw blended, continuous patterns that distinguish nucleosomes at one location (e.g., promoter nucleosomes) from those at another location (e.g., over the 3' ends of coding regions). These results are consistent with the idea of a simple, redundant histone code, in which multiple modifications share the same role.

Chromatin Immunoprecipitation↗

PubMed2004

Analysis of the activation status of Akt, NFkappaB, and Stat3 in human diffuse gliomas.

Loss of phosphatase and tensin homolog (PTEN) and amplification of the epidermal growth factor receptor (EGFR) gene contribute to the progression of gliomas. As downstream targets of the PTEN and EGFR signaling pathways, Akt, NFkappaB, and signal transducer and activator of transcription-3 (Stat3) have been shown to play important roles in the control of cell proliferation, apoptosis, and oncogenesis. We examined the activation status of Akt, NFkappaB, and Stat3 in 259 diffuse gliomas using tissue microarrays and immunohistochemistry, and evaluated their association with glioma grade. We observed significant positive correlations between the activation status of Akt and NFkappaB and glioma grade. In contrast, only focal immunoreactivity for phospho-Stat3 was observed in < 9% of high-grade gliomas. In addition, we observed a significant correlation between the activation of Akt and NFkappaB. Functional correlation between Akt activation and the activation of NFkappaB was confirmed in U251MG GBM cells in which inhibition of Akt activation either by stable expression of PTEN or by the PI3-kinase inhibitors, wortmannin and LY294002, led to a concomitant decrease in NFkappaB-binding activity. Thus, our results demonstrate that constitutive activation of Akt and NFkappaB, but not Stat3, contributes significantly to the progression of diffuse gliomas, and activation of Akt may lead to NFkappaB activation in high-grade gliomas.

Brain Neoplasms↗

PubMed2004

Differential gene expression and regulation of the bone morphogenetic protein antagonists follistatin and gremlin in normal and osteoarthritic human chondrocytes and synovial fibroblasts.

OBJECTIVE: To compare gene expression in normal and osteoarthritic (OA) human chondrocytes using microarray technology. Of the novel genes identified, we selected follistatin, a bone morphogenetic protein (BMP) antagonist, and investigated its expression/regulation as well as that of 3 other antagonists, gremlin, chordin, and noggin, in normal and OA chondrocytes and synovial fibroblasts. METHODS: Basal and induced gene expression were determined using real-time polymerase chain reaction. Gene regulation was monitored following treatment with inflammatory, antiinflammatory, growth, and developmental factors. Follistatin protein production was measured using a specific enzyme-linked immunosorbent assay, and localization of follistatin and gremlin in cartilage was determined by immunohistochemical analysis. RESULTS: All BMP antagonists except noggin were expressed in chondrocytes and synovial fibroblasts. Follistatin and gremlin were significantly up-regulated in OA chondrocytes but not in OA synovial fibroblasts. Chordin was weakly expressed in normal and OA cells. Production of follistatin protein paralleled the gene expression pattern. Follistatin and gremlin were expressed preferentially by the chondrocytes at the superficial layers of cartilage. Tumor necrosis factor alpha and interferon-gamma significantly stimulated follistatin expression but down-regulated expression of gremlin. Interleukin-1beta (IL-1beta) had no effect on follistatin but reduced gremlin expression. Conversely, BMP-2 and BMP-4 significantly stimulated expression of gremlin but down-regulated that of follistatin. IL-13, dexamethasone, transforming growth factor beta1, basic fibroblast growth factor, platelet-derived growth factor type BB, and endothelial cell growth factor down-regulated the expression of both antagonists. CONCLUSION: This study is the first to show the possible involvement of follistatin and gremlin in OA pathophysiology. The increased activin/BMP-binding activities of these antagonists could affect tissue remodeling. The data suggest that follistatin and gremlin might appear at different stages during the OA process, making them interesting targets for the treatment of this disease.

Bone Morphogenetic Protein 2↗

PubMed2004

Mapping of a discontinuous and highly conformational binding site on follicle stimulating hormone subunit-beta (FSH-beta) using domain Scan and Matrix Scan technology.

This paper describes the application of two novel screening technologies, i.e. Domain Scan (24- and 30-mer peptides) and Matrix Scan (24-mer peptides) technology, in the mapping of a discontinuous epitope on FSH-beta for a series of 20 monoclonal antibodies. 11 out of 20 mAb's, mapping of which was not successful by conventional Pepscan technology (12-mer peptides), showed selective binding to peptide-constructs corresponding to the beta3-loop of FSH in the Domain and/or Matrix Scan. Systematic replacement analysis studies with peptide-construct 57VYETVRVPGCAC-SAc-ADSLYTYPVATQ81 revealed that for most mAb's the amino acids R62, A70, D71, and L73 form the core of the epitope. A Domain Scan performed in the C-O format showed highly selective binding for mAb's 1 and 2 with only three beta1-beta3 peptide-constructs covering the residues 60TVRVPGCAHHADSLY74 in combination with 10IAIEKEECRFAI21, while for mAb 10 binding was observed with peptide-constructs containing the C-terminal residues 97RGLGPSYCSFGEMKE114 in combination with the residues 10IAIEKEECRFAI21. A Matrix Scan of mAb 17 showed that peptides from four different regions on FSH (1st strand beta3-loop, alpha 1-loop, long alpha2-loop, det. loop) showed enhanced binding in combination with several 70ADSL73-containing peptides. BIACORE measurements with mAb's 1, 2, 13, and 17 using a set of 21 different peptide(-construct)s partially confirmed the Domain and Matrix Scan screening results. Only 24- and 33-mer peptides covering both the 1st and 2nd strand of the beta3-loop showed measurable binding. Cyclic beta3-loop peptide mimics were found to bind significantly stronger (Kd approximately 5 microM) than the lineair analogues, in agreement with the fact that the discontinuous epitope is part of a loop structure. Coupling of the lineair beta1-peptide 1oIAIEKEECRFAI21 to the linear beta3-peptide *52TFKELVYETVRVPGCAHHADSLYTYPVATQAH83# via disulfide bond formation showed a 2-3 fold increase in Kd, thus conforming participation of the beta 1-loop in antibody binding for these mAb's.

Amino Acid Sequence↗

PubMed2002

Adapting arrays and lab-on-a-chip technology for proteomics.

The impact of proteomics as a discovery engine in life science and in drug discovery has increased tremendously over the last seven years. At the same time, proteomics has expanded from the initial trust as a two-dimensional gel based approach to cover more functional and structural properties of proteins. The development of lab-on-a-chip and protein arrays for proteomics will have to evolve with the changes in proteomics to stay relevant. Here, we review the changes in the field of proteomics and their impact on the development in protein arrays and lab-on-a-chip.

Antibodies↗

PubMed2002

Cell-free protein synthesis on a microchip.

We evaluated the expression of various proteins by using a cell-free protein synthesis system with a rapid translation system, a microtube, and a microchip technique. Protein expression was successfully achieved with a microfabricated reaction chamber on a plastic chip. Proteins were expressed effectively by use of expression vectors for T7 RNA polymerase (pET) instead of a plasmid for in vitro expression vector, which is recommended by the manufacture of the rapid translation system. Expression of the proteins depended on the type of proteins chosen. Two mammalian proteins were synthesized simultaneously with two expression vectors of pET species. Effective application of the cell-free protein synthesis system will enable miniaturization of protein synthesis and mediation between the transcriptome and proteome.

Animals↗