Proteomic Studies Using Microarrays

Feilner, Tanja; Kreutzberger, Jürgen; Niemann, Birgit; Kramer, Armin; Possling, Alexandra; Seitz, Harald; Kersten, Birgit

doi:10.2174/1570164043152768

Cited by 17 publications

(12 citation statements)

References 124 publications

(131 reference statements)

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“…Protein microarrays containing recombinant proteins have become an important high-throughput tool in the proteomics field because they allow parallel, fast and easy analysis of thousands of addressable immobilised proteins for phosphorylation or molecular interactions (Feilner et al 2004;Kersten et al 2004Angenendt 2005;Bertone and Snyder 2005;Merkel et al 2005;Stoll et al 2005;Hultschig et al 2006). Due to the small size of such microarrays, only minute amounts of spotted proteins and analytes are needed (Kreutzberger 2006).…”

Section: Protein Microarray Technologymentioning

confidence: 99%

“…We generated plant microarrays and established phosphorylation assays, first for barley (Kramer et al 2004) and later for Arabidopsis (Feilner et al 2005). This technology was subsequently used for the screening of potential substrates in large numbers of proteins.…”

Section: Establishment Of Protein Microarrays For Phosphorylation Stumentioning

confidence: 99%

“…In this chapter we will focus on protein microarrays, which have been used mainly to identify potential phosphorylation targets of different plant kinases, first in barley (Kramer et al 2004) and later in Arabidopsis thaliana (Feilner et al 2005). Protein kinases are enzymes that modify other proteins via the chemical addition of phosphate groups.…”

Section: Introductionmentioning

confidence: 99%

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Plant Proteomics

Dumas‐Gaudot¹,

Recorbet²

2007

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EditorsJozef Šamaj received his Ph.D. degree in Plant Physiology from the Comenius University in Bratislava, Slovakia. He completed three post-doctoral programmes supported by Eurosilva, the Alexander von Humboldt Foundation, and the EU Marie Curie Programme in the highly regarded laboratories of Alain Boudet in Toulouse, Dieter Volkmann in Bonn, and Heribert Hirt in Vienna. He worked on the cell biology of somatic embryogenesis, lignifi cation in tree species, arabinogalactan proteins, the cytoskeleton, and signalling proteins. Jozef Šamaj has co-edited three books and co-authored more than 75 research papers, reviews, and book chapters. He is a senior lecturer and group leader at the Institute of Cellular and Molecular Botany in Bonn, Germany, and senior researcher at the Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia. His current research is focussed on the role of signalling components and the cytoskeleton in relation to the vesicular traffi cking during plant development and stress responses using integrated cell-biological and functional proteomics approaches. Jozef Šamaj Jay Thelen v Jay Thelen received his B.Sc. degree in Biology and Biochemistry from the University of Nebraska-Lincoln in 1993. He earned his Ph.D. from the University of Missouri-Columbia (UMC) studying the structure and regulation of plant mitochondrial pyruvate dehydrogenase complexes under the guidance of Douglas Randall. In 1999 he started a 3-year postdoctoral position in John Ohlrogge's lab at Michigan State University investigating the plastid acetyl-CoA carboxylase protein complex. He returned to UMC in 2002 as the Associate Director of a campus Proteomics Center. In 2004, he was promoted to Assistant Professor in the Biochemistry Department, a position he currently holds. He has authored or co-authored 35 research and review articles since 1994. His research interests are centered around the regulation of plant metabolism, particularly carbon assimilation in oilseeds, and multienzyme metabolic complexes. He is currently studying seed fi lling in numerous crop oilseeds, using various quantitative proteomics approaches. He is also investigating global phosphoprotein networks involved in seed development and is developing improved strategies for quantitative proteomics.

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Section: Protein Microarray Technologymentioning

confidence: 99%

Section: Establishment Of Protein Microarrays For Phosphorylation Stumentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Plant Proteomics

Dumas‐Gaudot¹,

Recorbet²

2007

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“…Recent technological developments like protein microarrays or biosensor analyses using surface plasmon resonance (SPR) allow protein-protein interactions to be characterized with high accuracy and with reasonable throughput [7,8]. With the Biacore technology binding partners can be detected in real time and separate kinetic parameters for the association and dissociation phases can be derived.…”

Section: Introductionmentioning

confidence: 99%

Differential binding studies applying functional protein microarrays and surface plasmon resonance

et al. 2006

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A variety of different in vivo and in vitro technologies provide comprehensive insights in proteinprotein interaction networks. Here we demonstrate a novel approach to analyze, verify and quantify putative interactions between two members of the S100 protein family and 80 recombinant proteins derived from a proteome-wide protein expression library. Surface plasmon resonance (SPR) using Biacore technology and functional protein microarrays were used as two independent methods to study protein-protein interactions. With this combined approach we were able to detect nine calcium-dependent interactions between Arg-Gly-Ser-(RGS)-His 6 tagged proteins derived from the library and GST-tagged S100B and S100A6, respectively. For the protein microarray affinity-purified proteins from the expression library were spotted onto modified glass slides and probed with the S100 proteins. SPR experiments were performed in the same setup and in a vice-versa approach reversing analytes and ligands to determine distinct association and dissociation patterns of each positive interaction. Besides already known interaction partners, several novel binders were found independently with both detection methods, albeit analogous immobilization strategies had to be applied in both assays.

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“…Because protein arrays allow the parallel detection of addressable elements in a single experiment (12)(13)(14)(15)(16)(17)(18), they have been recognized as a promising technology for the identification of PPIs (19,20) or other specific biochemical activities (20 -23), and much effort has been devoted to their development in recent years. Zhu et al (20) e.g.…”

mentioning

confidence: 99%

Identification of VCP/p97, Carboxyl Terminus of Hsp70-interacting Protein (CHIP), and Amphiphysin II Interaction Partners Using Membrane-based Human Proteome Arrays

Grelle

Kostka

Otto

et al. 2006

Molecular & Cellular Proteomics

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Proteins mediate their biological function through interactions with other proteins. Therefore, the systematic identification and characterization of protein-protein interactions have become a powerful proteomic strategy to understand protein function and comprehensive cellular regulatory networks. For the screening of valosin-containing protein, carboxyl terminus of Hsp70-interacting protein (CHIP), and amphiphysin II interaction partners, we utilized a membrane-based array technology that allows the identification of human protein-protein interactions with crude bacterial cell extracts. Many novel interaction pairs such as valosin-containing protein/autocrine motility factor receptor, CHIP/caytaxin, or amphiphysin II/DLP4 were identified and subsequently confirmed by pull-down, two-hybrid and co-immunoprecipitation experiments. In addition, assays were performed to validate the interactions functionally. CHIP e.g. was found to efficiently polyubiquitinate caytaxin in vitro, suggesting that it might influence caytaxin degradation in vivo. Using peptide arrays, we also identified the binding motifs in the proteins DLP4, XRCC4, and fructose-1,6-bisphosphatase, which are crucial for the association with the Src homology 3 domain of amphiphysin II. Together these studies indicate that our human proteome array technology permits the identification of protein-protein interactions that are functionally involved in neurodegenerative disease processes, the degradation of protein substrates, and the transport of membrane vesicles. Molecular & Cellular Proteomics 5:234 -244, 2006.As protein-protein interactions (PPIs) 1 are central to most biological processes, their systematic identification is considered a key strategy for uncovering the complex organization principles of functional cellular networks (1-3). A number of experimental and computational techniques have been developed to determine all the potential and actual PPIs in selected model organisms (4 -8) and humans (9 -11).Because protein arrays allow the parallel detection of addressable elements in a single experiment (12-18), they have been recognized as a promising technology for the identification of PPIs (19,20) or other specific biochemical activities (20 -23), and much effort has been devoted to their development in recent years. Zhu et al. (20) e.g. printed 5,800 purified yeast proteins onto coated glass slides and used them successfully in proof-of-principle experiments for the detection of novel calmodulin-and phospholipid-interacting proteins. Protein arrays were also used efficiently for identifying novel targets of protein kinases (24 -26). In principle, the production of protein arrays and their utilization for systematic large scale interaction and activity screens has proven viable. One major drawback, however, has been the necessity to use purified proteins. Protein purification is usually difficult, time-consuming, and expensive. For array-based studies, especially high throughput systematic screening (19), technologies are needed that permit...

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Proteomic Studies Using Microarrays

Cited by 17 publications

References 124 publications

Plant Proteomics

Plant Proteomics

Differential binding studies applying functional protein microarrays and surface plasmon resonance

Identification of VCP/p97, Carboxyl Terminus of Hsp70-interacting Protein (CHIP), and Amphiphysin II Interaction Partners Using Membrane-based Human Proteome Arrays

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