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Results for “Protein Array Analysis”

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PubMed2003

In vitro protein microarrays for detecting protein-protein interactions: application of a new method for fluorescence labeling of proteins.

Protein microarrays or proteome chips are potentially powerful tools for comprehensive analysis of protein-protein interactions. In interaction analysis, a set of immobilized proteins is arrayed on slides and each slide is probed with a set of fluorescently labeled proteins. Here we have developed and tested an in vitro protein microarray, in which both arraying and probing proteins were prepared by cell-free translation. The in vitro synthesis of fluorescently labeled proteins was accomplished by a new method: a fluorophore-puromycin conjugate was incorporated into a protein at the C-terminus on the ribosome. The resulting fluorescently labeled proteins were confirmed to be useful for probing protein-protein interactions on protein microarrays in model experiments. Since the in vitro protein microarrays can easily be extended to a high-throughput format and also combined with in vitro display technologies such as the streptavidin-biotin linkage in emulsions method (Doi and Yanagawa, FEBS Lett. 1999, 457, 227-230), our method should be useful for large-scale analysis of protein-protein interactions.

Animals↗
PubMed2003

Methods for on-chip protein analysis.

The unambiguous identification of peptides/proteins is crucial for the definition of the proteome. Using ProteinChip Array technology also known as surface-enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF MS), we developed experimental protocols and probed test conditions required for the protein identification on ProteinChip surfaces. We were able to directly digest peptides/proteins on-chip surfaces by specific proteases, such as trypsin, and to obtain the peptide mass fingerprint of the sample under investigation by its direct analysis on a simple laser desorption/ionization mass spectrometer. Furthermore, tandem mass spectrometry was performed on several of the resulting tryptic peptides by using collision quadrupole time of flight (Qq-TOF) MS/MS via the ProteinChip interface, thus allowing the unambiguous identification of the protein(s) within the sample. In addition, we were able to identify the C-terminal sequence of peptides by their digestion with carboxypeptidase Y directly on ProteinChip surfaces coupled with SELDI-TOF MS analysis of the resulting peptide mass ladders employing the instrument's protein ladder sequence software. Moreover, the removal of up to nine amino acid residues from the C-terminal end of a peptide extends the functional range of Qq-TOF MS/MS sequence determination to over 3000 m/z. The utility of these procedures for the proteome exploration are discussed.

Amino Acid Sequence↗
PubMed2003

Antibody-based technologies for target discovery.

Antibodies have proven to be exquisite investigation tools in the field of life sciences. They also constitute one of the oldest and most successful biological products for diagnostics and therapeutics. This review investigates the current use of antibodies in target discovery. To address this topic in a larger context, established and emerging technologies that are expected to contribute to target discovery will first be examined. These technologies include: mass spectroscopic analysis of proteins, protein-protein interaction and other network analysis approaches, as well as protein and antibody arrays. The potential of antibody engineering and the ANTIBIOMIX technology will then be discussed; antibody therapeutics, however, will not be examined.

Animals↗
PubMed2003

Protein arrays: the current state-of-the-art.

The completion of projects for sequencing whole genomes such as those of human, Saccaromyces cerevisiae and Caenorhabditis elegans has led to a rapid increase in the availability of genetic information. The technology by which such information is acquired is having a major impact on the way we think about analysing the RNA and protein products of the gene transcription. Transcriptome analysis has, via microarray technology, managed to achieve a near genomic scale quantitative analysis of mRNA levels. Several other technologies such as quantitative reverse transcriptase polymerase chain reaction and representational differential analysis are also available for analysing gene products. Traditionally, protein analysis has been performed by assaying one particular protein at a time, with very little parallel analysis. As protein function is a direct consequence of the protein product of the gene and as mRNA levels do not always correlate well with protein, it is desirable to analyse the entire protein complement of a cell etc. on a similar scale to mRNA. Despite the clear interest in analysing the expression, structure and function of proteins at a genomic scale, they have proven less amenable to such generic, high-throughput approaches. This review highlights the current thinking in the area of proteome analysis and considers the potential for future technology development in the area of protein arrays.

Animals↗
PubMed2002

Protein microarrays to detect protein-protein interactions using red and green fluorescent proteins.

Proteomics, the study of protein function on a global scale, will play an important role in furthering our understanding of gene functions, complex biological pathways, and discovery of novel drug targets. A number of techniques have been developed for proteomic studies to identify and analyze proteins, compare protein expression levels, and study protein-protein interactions. Recent developments have applied a DNA array-type approach to immobilize proteins on a surface for high-throughput analysis. Here we report the development and construction of protein chips using derivatized glass and nitrocellulose-coated slides and the employment of recombinant proteins fused with green and red fluorescent proteins for detection. Fluorescent signals were found to be proportional to the amount of arrayed proteins and could be readily detected with a conventional fluorescence slide scanner. This technique allows the investigation of protein-protein interactions without the need for additional labeling steps of probe proteins.

Antibodies↗
PubMedDate not supplied

Measuring protein interactions by microchip self-interaction chromatography.

The self-interaction of proteins is of paramount importance in aggregation and crystallization phenomena. Solution conditions leading to a change in the state of aggregation of a protein, whether amorphous or crystalline, have mainly been discovered by the use of trial and error screening of large numbers of solutions. Self-interaction chromatography has the potential to provide a quantitative method for determination of protein self-interactions amenable to high-throughput screening. This paper describes the construction and characterization of a microchip separation system for low-pressure self-interaction chromatography using lysozyme as a model protein. The retention time was analyzed as a function of mobile-phase composition, amount of protein injected, flow rate, and stationary-phase modification. The capacity factors (k') as a function of crystallizing agent concentration are compared with previously published values for the osmotic second virial coefficient (B(22)) obtained by static light scattering, showing the ability of the chip to accurately determine protein-protein interactions. A 500-fold reduction in protein consumption and the possibility of using conventional instrumentation and automation are some of the advantages over currently used methodologies for evaluating protein-protein interactions.

Chromatography↗
PubMed2003

Surface plasmon resonance mass spectrometry: recent progress and outlooks.

The combination of surface plasmon resonance (SPR) and mass spectrometry (MS) has created a unique approach to protein investigations. Surface plasmon resonance is used to quantify interactions between proteins and surface-immobilized ligands, and MS is used to determine the structural features of the bound proteins. Recent progress in SPR-MS includes improved methods and operations, increased limits of detection, multi-protein analysis and protein-complex delineation. With the subsequent design of SPR protein arrays, SPR-MS is expected to enter into the field of high-throughput protein interaction discovery and miniaturized diagnostics.

Mass Spectrometry↗
PubMed2003

Recent developments in analytical and functional protein microarrays.

In recent years, the genomes of many different organisms have been fully sequenced and annotated. As a consequence of this information, a number of methods have emerged to study the function of many genes and proteins in parallel. One recent approach for the large-scale analysis of proteins is the use of protein microarrays in which hundreds to thousands of proteins are arrayed and assayed simultaneously. Protein arrays can be used for assessing protein levels and following disease markers, identifying biochemical activities, analyzing post-translational modifications, building interaction networks, and for drug discovery and development. In this review, we discuss the construction of different types of protein arrays, and their numerous and diverse applications.

Antibodies↗
PubMed2000

Expression profiling of pancreatic beta cells: glucose regulation of secretory and metabolic pathway genes.

Pancreatic beta cells respond to changes in blood glucose by secreting insulin and increasing insulin synthesis. To identify genes used in these responses, we have carried out expression profiling of beta cells exposed to high (25 mM) or low (5.5 mM) glucose by using oligonucleotide microarrays. Functional clustering of genes that averaged a 2.2-fold or greater change revealed large groups of secretory pathway components, enzymes of intermediary metabolism, cell-signaling components, and transcription factors. Many secretory pathway genes were up-regulated in high glucose, including seven members of the endoplasmic reticulum (ER) translocon. In agreement with array analysis, protein levels of translocon components were increased by high glucose. Most dramatically, the alpha subunit of the signal recognition particle receptor was increased over 20-fold. These data indicate that the translocon and ribosome docking are major regulatory targets of glucose in the beta cell. Analysis of genes encoding enzymes of intermediary metabolism indicated that low glucose brought about greater utilization of amino acids as an energy source. This conclusion was supported by observations of increased urea production under low-glucose conditions. The above results demonstrate genome-wide integration of beta-cell functions at the level of transcript abundance and validate the efficacy of expression profiling in identifying genes involved in the beta-cell glucose response.

Animals↗
PubMed2002

Protein and peptide array analysis of autoimmune disease.

Molecular cloning, sequencing of the human genome, and other major advances in biomedical research have contributed substantially to our understanding of autoimmune disease. Nevertheless, to date, such advances have failed to reveal the etiology of or yield curative therapies for autoimmune disease. New approaches are needed. Proteomics, the large-scale study of expression and function of proteins that compose our tissues and mediate disease, represents a powerful and promising strategy. We developed protein and peptide arrays to profile autoantibody responses in autoimmune disease. Protein and peptide array analysis of autoimmune samples is revealing human and pathogen proteins involved in initiation and perpetuation of autoimmunity. Proteomic determination of autoantibody profiles can be utilized for diagnosis, prognostication, and guiding tolerizing therapy for autoimmune disease.

Antigens↗
PubMed2003

Proteomics.

PURPOSE OF REVIEW: Proteomics encompasses a group of technologies that attempt to separate, identify and characterize a global set of proteins. This review will highlight the technologies available, outline the capabilities, advantages and disadvantages of each and briefly describe applications in nephrology. RECENT FINDINGS: Proteomics provides information about abundance, location, chemical modification and protein-protein interactions that is not available from genomic technologies. Several proteomic approaches are now widely available. Liquid chromatography/mass spectrometry, two-dimensional gel electrophoresis, antibody arrays and protein chips (surface enhanced laser desorption ionization) provide opportunities to identify and compare an abundance of proteins as well as to determine posttranslational modifications, subcellular location and molecular interactions. Recent advances such as multidimensional chromatographic analysis and isotope coded affinity tags have expanded the usefulness of these approaches. SUMMARY: Proteomic technologies are improving and developing rapidly. These techniques will be valuable tools to develop markers for disease, identify and evaluate proteins as drug targets and understand renal physiology at the protein level.

Antibodies↗
PubMed2002

Global profiling of the cell surface proteome of cancer cells uncovers an abundance of proteins with chaperone function.

There is currently limited data available pertaining to the global characterization of the cell surface proteome. We have implemented a strategy for the comprehensive profiling and identification of surface membrane proteins. This strategy has been applied to cancer cells, including the SH-SY5Y neuroblastoma, the A549 lung adenocarcinoma, the LoVo colon adenocarcinoma, and the Sup-B15 acute lymphoblastic leukemia (B cell) cell lines and ovarian tumor cells. Surface membrane proteins of viable, intact cells were subjected to biotinylation then affinity-captured and purified on monomeric avidin columns. The biotinylated proteins were eluted from the monomeric avidin columns as intact proteins and were subsequently separated by two-dimensional PAGE, transferred to polyvinylidene difluoride membranes, and visualized by hybridization with streptavidin-horseradish peroxidase. Highly reproducible, but distinct, two-dimensional patterns consisting of several hundred biotinylated proteins were obtained for the different cell populations analyzed. Identification of a subset of biotinylated proteins among the different cell populations analyzed using matrix-assisted laser desorption ionization and tandem mass spectrometry uncovered proteins with a restricted expression pattern in some cell line(s), such as CD87 and the activin receptor type IIB. We also identified more widely expressed proteins, such as CD98, and a sushi repeat-containing protein, a member of the selectin family. Remarkably, a set of proteins identified as chaperone proteins were found to be highly abundant on the cell surface, including GRP78, GRP75, HSP70, HSP60, HSP54, HSP27, and protein disulfide isomerase. Comprehensive profiling of the cell surface proteome provides an effective approach for the identification of commonly occurring proteins as well as proteins with restricted expression patterns in this compartment.

Activin Receptors, Type II↗
PubMed2002

The challenges of developing a sound proteomics strategy.

This paper will review the challenges of developing a proteomics strategy. A key issue is the integration of the two-dimensional (2-D) gel platform with mass spectrometry measurements. The use of both matrix-assisted laser/desorption ionization (on off-line coupling) and electrospray (on-line) ionization are complementary. While the use of one-dimensional and 2-D gels are essential to many aspects of proteomics research (sample preparation, preliminary fractionation and quantitation, storage of protein components), the emergence of shotgun sequencing based on high performance liquid chromatography and tandem mass spectrometry offers a powerful new approach. The latter has particular utility in the characterization of low level samples and complex post-translational modifications. The development of capillary columns, such as 75 to 150 micron, that can be packed in a reproducible manner has been a key step in the development of high sensitivity liquid chromatography/mass spectrometry analysis.

Chromatography↗
PubMedDate not supplied

Solid supports for microarray immunoassays.

Stimulated by the achievements of the first phase in genomics and the resulting need of assigning functions to the acquired sequence information, novel formats of immunoassays are being developed for high-throughput multi-analyte studies. In principle, they are similar in nature to the microarray assays already established at the level of nucleic acids. However, the biochemical diversity and the sheer number of proteins are such that an equivalent analysis is much more complex and thus difficult to accomplish. The wide range of protein concentration complicates matters further. Performing microarray immunoassays already represents a challenge at the level of preparing a working chip surface. Arrays have been produced on filter supports, in microtiter plate wells and on glass slides, the last two usually coated with one-, two- or three-dimensionally structured surface modifications. The usefulness and suitability of all these support media for the construction and application of antibody microarrays are reviewed in this manuscript in terms of the different kinds of immunoassay and the various detection procedures. Additionally, the employment of microarrays containing alternative sensor molecules is discussed in this context. The sensitivity of microspot immunoassays predicted by the current analyte theory is not yet a reality, indicating the extent of both the technology's potential and the size of the task still ahead.

Acrylic Resins↗
PubMed2003

Protein analysis on a proteomic scale.

The long-term challenge of proteomics is enormous: to define the identities, quantities, structures and functions of complete complements of proteins, and to characterize how these properties vary in different cellular contexts. One critical step in tackling this goal is the generation of sets of clones that express a representative of each protein of a proteome in a useful format, followed by the analysis of these sets on a genome-wide basis. Such studies enable genetic, biochemical and cell biological technologies to be applied on a systematic level, leading to the assignment of biochemical activities, the construction of protein arrays, the identification of interactions, and the localization of proteins within cellular compartments.

Animals↗
PubMed2002

Effect of rosiglitazone on the differential expression of diabetes-associated proteins in pancreatic islets of C57Bl/6 lep/lep mice.

The insulin sensitizer drug, rosiglitazone, has been shown to have a protective effect on pancreatic islet cell structure and function in animal models of type 2 diabetes. The identification of new molecular targets associated both with islet cell dysfunction and protection is a crucial research goal. In the present study, a proteomics approach has been used to identify such targets. Obese C57Bl/6J lep/lep mice and lean littermates were given the insulin sensitizer drug BRL49653, rosiglitazone. It normalized the impaired glucose tolerance in lep/lep mice but had no significant effect on glucose tolerance in the lean mice. Pancreatic islet polypeptides were arrayed by a two-dimensional gel electrophoresis system that separated more than 2500 individual spots. Three overexpressed and six underexpressed proteins were significant (p < 0.05) between lep/lep and lean mice, and four were modulated significantly (p < 0.05) by the rosiglitazone treatment of the obese mice. The identity of these differentially expressed proteins was made using mass spectrometric analysis and provided evidence that differential expression of actin-binding proteins may be an important aspect of defective islet function. Rosiglitazone increased carboxypeptidase B expression in both lep/lep and normal mice suggesting that this might be an independent effect of rosiglitazone that contributes to improved insulin processing.

Animals↗