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Results for “Protein Array Analysis”

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At least 433 records · Page 24Linked to original sources
PubMed2006

Label-free reading of microarray-based proteins with high throughput surface plasmon resonance imaging.

A simple method is presented discriminating proteins at a gold surface by using an emerging technology, surface plasmon resonance (SPR) imaging. As a high throughput method, the protein array of bovine serum albumin (BSA), poly-l-lysine (PL), casein and lactate dehydrogenase (LDG) was fabricated and SPR imaging enables detection from different kinds of proteins immobilized on the sensor surface. These proteins can be discriminated directly by various reflected intensity or changing the incident angular position of light. Denaturation of these immobilized proteins on SPR sensor by interacting with denaturant 6M GdnHCl solution was also performed and obvious changes in reflected intensity were occurred after denaturation. The observation of denaturation of these proteins further supported the fact that different proteins could be discriminated on protein array before denaturation. On the other hand, the procedure of denaturation provided useful information that any change of molecular structure with the progress of denaturation would result in change of SPR signal. Excellent reproducibility with a chip-to-chip for label-free discriminating various proteins was achieved.

Image Enhancement↗
PubMed2004

Improving the intein-mediated, site-specific protein biotinylation strategies both in vitro and in vivo.

One of the critical issues in the generation of a protein microarray lies in the choice of immobilization strategies, which ensure proteins are adhered to the glass surface while properly retaining their native biological activities. We previously developed intein-mediated strategies for protein biotinylation and site-specific protein microarray generation. Herein, we report new findings of these strategies, which improve the biotinylation efficiency of proteins by up to 10-folds.

Biotin↗
PubMed2005

Site-specific immobilization of proteins in a microarray using intein-mediated protein splicing.

One of the critical issues in the generation of a protein microarray lies in the choice of immobilization strategies, which ensure proteins are adhered to the glass surface while properly retaining their native biological activities. Herein, we report a bacterium-based, intein-mediated strategy to generate N-terminal cysteine-containing proteins which are then chemoselectively immobilized to a thioester-functionalized glass slide to generate the corresponding protein microarray. We also showed preliminary data of the strategy in a yeast host system.

Electrophoresis, Polyacrylamide Gel↗
PubMed2006

Protein microarrays to study carbohydrate-recognition events.

In order to expand areas in which protein microarrays can be used to solve important biological problems, we have investigated ways in which the technique can be employed for functional glycomics. Initially, our protein microarrays were used for the rapid identification of carbohydrate-binding proteins using trifunctional carbohydrate probes and fluorescent dye-labeled polysaccharides. Glycan probes were selectively bound to the corresponding lectins immobilized on the solid surface. In addition, these microarrays were also employed for profiling of carbohydrates on Jurkat T-cell surfaces. These cells adhered to ConA, RCA(120), SNA and WGA, indicating expression of alpha-Man, Gal, NeuNAcalpha2,6Gal and GlcNAc residues on their surfaces. Furthermore, we determined binding affinities between WGA and carbohydrates by measuring IC(50) values of GlcNAc that inhibited 50% of trivalent GlcNAc binding to WGA immobilized on the solid surface. All the experiments show that protein microarrays can be used to study carbohydrate-recognition events in the field of glycomics.

Carbohydrates↗
PubMed2004

Functional protein microarrays: ripe for discovery.

The manufacture and use of protein microarrays with correctly folded and functional content presents significant challenges. Despite this, the feasibility and utility of such undertakings are now clear, and exciting progress has recently been demonstrated in the areas of content generation, printing strategies and protein immobilization. More importantly, we are now beginning to enjoy the fruits of these efforts as functional protein microarrays are being increasingly employed for biological discovery purposes. Recent examples of this include the characterization of autoantibody responses, antibody specificity profiling, protein-protein domain interaction profiling and a comprehensive characterization of coiled-coil interactions. The best, however, is yet to come.

Animals↗
PubMed2004

Exploring the range of protein flexibility, from a structural proteomics perspective.

Changes in protein conformation play a vital role in biochemical processes, from biopolymer synthesis to membrane transport. Initial systematizations of protein flexibility, in a database framework, concentrated on the movement of domains and linkers. Movements were described in terms of simple sliding and hinging mechanisms of individual secondary structural elements. Recently, the accelerated pace and sophistication of methods for structural characterization of proteins has allowed high-resolution studies of increasingly complex assemblies and conformational changes. New data emphasize a breadth of possible structural mechanisms, particularly the ability to drastically alter protein architecture and the native flexibility of many structures.

Pliability↗
PubMed2004

Peptide arrays: towards routine implementation.

Peptide arrays have attracted wide interest as tools for discovering biochemical interactions. Because many protein binding and enzyme activities are directed towards peptides, the preparation of arrays having hundreds to thousands of immobilized peptides offers an unprecedented opportunity for identifying interactions of proteins. This short opinion reviews recent progress in the preparation of peptide arrays and their use in the characterization of biomolecular interactions and the discovery of new reagents for biological researches. This body of work establishes the feasibility of this technology and suggests that it will find much wider use in research groups.

Biotechnology↗
PubMed2005

Protein microarrays as tools for functional proteomics.

Protein microarrays present an innovative and versatile approach to study protein abundance and function at an unprecedented scale. Given the chemical and structural complexity of the proteome, the development of protein microarrays has been challenging. Despite these challenges there has been a marked increase in the use of protein microarrays to map interactions of proteins with various other molecules, and to identify potential disease biomarkers, especially in the area of cancer biology. In this review, we discuss some of the promising advances made in the development and use of protein microarrays.

Protein Array Analysis↗
PubMed2005

Protein components for nanodevices.

A long-term goal of nanobiotechnology is to build tiny devices that respond to the environment, perform computations and carry out tasks. Considerable progress has been made in building protein components for such devices, and here we describe examples, including self-assembling protein arrays, pores with triggers and switches, and motor proteins harnessed for specific tasks. A major issue that has been successfully addressed in this recent work is the interface between the proteins and other components of the system, such as a metal surface. While further progress is expected in the coming years, the assembly of devices from the components has seen more limited accomplishments. For example, although a wide variety of sensors based on nanobiotechnology has been developed, unresolved problems still confront the construction of complex nanobioelectronic circuits, and the development of nanorobotics with biological components remains a distant dream.

Microchip Analytical Procedures↗
PubMed2006

Chemical technologies for probing glycans.

Glycans are central to many biological processes, but efforts to define their functions at the molecular level have been frustrated by a lack of suitable technologies. Here we highlight chemical tools that are beginning to address this need.

Carbohydrate Conformation↗
PubMed2004

A hot spot for protein kinase inhibitor sensitivity.

ATP binding site-directed protein kinase inhibitors are potent weapons in the war on cancer. However, specific mutations at an inhibitor-sensitivity "hot spot" can render these molecules ineffective. In this issue of Chemistry & Biology, Daub and coworkers have used an array of known kinase inhibitors to systematically characterize the desensitizing effects of hot spot mutations.

Antineoplastic Agents↗
PubMed2004

Transformation of low-affinity lead compounds into high-affinity protein capture agents.

A simple and potentially general approach to the isolation of high-affinity and -specificity protein binding synthetic molecules is presented. A modest affinity lead compound is appended to the end of each molecule in a combinatorial library of oligomeric compounds, such as peptides or peptoids. The library is then screened under conditions too demanding for the lead to support robust binding to the protein target. It was anticipated that this procedure would select for bivalent ligands in which the oligomer library provides both a second binding element as well as an appropriate linker between this element and the lead compound. We report here synthetic ligands for the Mdm2 protein and ubiquitin able to capture their target proteins from dilute solutions in the presence of a large excess of other proteins.

Amino Acid Sequence↗
PubMed2006

A wavelet-based data pre-processing analysis approach in mass spectrometry.

Recently, mass spectrometry analysis has a become an effective and rapid approach in detecting early-stage cancer. To identify proteomic patterns in serum to discriminate cancer patients from normal individuals, machine-learning methods, such as feature selection and classification, have already been involved in the analysis of mass spectrometry (MS) data with some success. However, the performance of existing machine learning methods for MS data analysis still needs improving. The study in this paper proposes a wavelet-based pre-processing approach to MS data analysis. The approach applies wavelet-based transforms to MS data with the aim of de-noising the data that are potentially contaminated in acquisition. The effects of the selection of wavelet function and decomposition level on the de-noising performance have also been investigated in this study. Our comparative experimental results demonstrate that the proposed de-noising pre-processing approach has potentials to remove possible noise embedded in MS data, which can lead to improved performance for existing machine learning methods in cancer detection.

Algorithms↗
PubMed2005

Functional protein microarrays: just how functional are they?

Arrays of immobilized proteins have been developed for the discovery and characterization of protein functions ranging from molecular recognition to enzymatic activity. The success of these applications is highly dependent upon the maintenance of protein structure and function while in an immobilized state - a largely untested hypothesis. However, the immobilization of functional proteins is not without precedent. Active enzymes have been successfully immobilized for industrial applications for several decades. Furthermore, a survey of recent protein microarray literature reveals that an even wider range of proteins can maintain 'proper' function while immobilized. These reports help to validate the functionality of so-called functional protein microarrays.

DNA-Binding Proteins↗
PubMed2006

Protein-mediated nanoscale biotemplating.

Biomimetics--the concept of taking ideas from nature and implementing them in technology--has found particular use for the development of nanoscale materials. One such approach employs protein-mediated biotemplating for the nanostructuring of inorganic material. Recently, two key advances have been witnessed in this field. Firstly, the number of successfully employed biotemplates, including feasibility demonstrations of using three-dimensional crystalline structures, has been expanded. Secondly, the introduction of site-directed mutations on the protein template, or the display of peptides that exhibit effective biorecognition sequences for inorganic structures, has led to substantial improvements in our ability to control protein-mediated biotemplating. Taken together, these achievements will pave the way for the successful application of protein-mediated biotemplating in the future.

Binding Sites↗
PubMed2006

Nanoscale biocatalyst systems.

Since the large-scale application of immobilized enzymes in the 1960s, substantial research efforts have aimed to optimize the structure of carrier materials for better catalytic efficiency. In this regard, nanoscale materials provide the upper limits in balancing the key factors that determine the efficiency of biocatalysts, including surface area, mass transfer resistance, and effective enzyme loading. Various nanomaterials, such as nanoparticles, nanofibers, nanotubes and nanoporous matrices, have shown potential for revolutionizing the preparation and use of biocatalysts. Beyond their high surface area:volume ratios, nanoscale biocatalyst systems exhibit unique behaviors that distinguish them from traditional immobilized systems. The Brownian motion of nanoparticles, confining effect of nanopores and self-assembling behaviors of discrete nanostructures are providing exciting opportunities in this field. The development of catalyst systems that are highly stable and efficient, capable of self-targeting or that function as molecular machines to catalyze multiple reactions is rapidly reshaping our vision of biocatalysts.

Binding Sites↗