ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome

Taussig, Michael J.; Stoevesandt, Oda; Borrebaeck, Carl; Bradbury, Andrew; Cahill, Dolores J.; Cambillau, Christian; Daruvar, Antoine de; Dübel, Stefan; Eichler, Jutta; Frank, Ronald; Gibson, Toby J.; Gloriam, David E.; Gold, Larry; Herberg, Friedrich W.; Hermjakob, Henning; Hoheisel, Jörg D.; Joos, Thomas; Kallioniemi, Olli; Koegl, Manfred; Konthur, Zoltán; Korn, Bernhard; Kremmer, Elisabeth; Krobitsch, Sylvia; Landegren, Ulf; Maarel, Silvère M. van der; McCafferty, John; Muyldermans, Serge; Nygren, Per‐Åke; Palcy, Sandrine; Plückthun, Andreas; Polić, Bojan; Przybylski, Michael; Saviranta, Petri; Sawyer, Alan; Sherman, David James; Skerra, Arne; Templin, Markus F.; Ueffing, Marius; Uhlén, Mathias

doi:10.1038/nmeth0107-13

Cited by 220 publications

(169 citation statements)

References 38 publications

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“…If one of the affinity reagents could be generated by the strategy used here involving the generation of affinity-purified monospecific antibodies, the other affinity reagent should thus be generated with an alternative technology platform, preferably generating a renewable resource of reagents available to the scientific community. This emphasizes the need for international efforts to coordinate such antibody-based efforts as previously discussed by Haab et al (28) and Taussig et al (29).…”

Section: Discussionmentioning

confidence: 75%

A Genecentric Human Protein Atlas for Expression Profiles Based on Antibodies

Berglund

Björling

Oksvold

et al. 2008

Molecular & Cellular Proteomics

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570

458

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An attractive path forward in proteomics is to experimentally annotate the human protein complement of the genome in a genecentric manner. Using antibodies, it might be possible to design protein-specific probes for a representative protein from every protein-coding gene and to subsequently use the antibodies for systematical analysis of cellular distribution and subcellular localization of proteins in normal and disease tissues. A new version (4.0) of the Human Protein Atlas has been developed in a genecentric manner with the inclusion of all human genes and splice variants predicted from genome efforts together with a visualization of each protein with characteristics such as predicted membrane regions, signal peptide, and protein domains and new plots showing the uniqueness (sequence similarity) of every fraction of each protein toward all other human proteins. The new version is based on tissue profiles generated from 6120 antibodies with more than five million immunohistochemistry-based images covering 5067 human genes, corresponding to ϳ25% of the human genome. Version 4.0 includes a putative list of members in various protein classes, both functional classes, such as kinases, transcription factors, G-protein-coupled receptors, etc., and project-related classes, such as candidate genes for cancer or cardiovascular diseases. The exact antigen sequence for the internally generated antibodies has also been released together with a visualization of the application-specific validation performed for each antibody, including a protein array assay, Western blot analysis, immunohistochemistry, and, for a large fraction, immunofluorescencebased confocal microscopy. New search functionalities have been added to allow complex queries regarding protein expression profiles, protein classes, and chromosome location. The new version of the protein atlas thus is a resource for many areas of biomedical research, including protein science and biomarker discovery. Molecular

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Section: Discussionmentioning

confidence: 75%

A Genecentric Human Protein Atlas for Expression Profiles Based on Antibodies

Berglund

Björling

Oksvold

et al. 2008

Molecular & Cellular Proteomics

Self Cite

570

458

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“…Protein modifications finely tune protein functions, by causing changes in protein activity, cellular localization, and interactions with other proteins (29). Thus, binding proteins that target sites of PTMs or specifically recognize changes in tertiary and quaternary structures of modified proteins would be valuable tools both to detect different protein states and to interfere with their function in living cells (4). In contrast to antibodies and their derivatives, DARPins Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Also, the detection of modifications by MS is still far from comprehensive. Thus, the creation of collections of specific binding molecules targeting a great number of individual proteins, including variants and modifications, will become equally important (4). Such specific affinity reagents would not only be beneficial for traditional biochemical approaches detecting protein modifications and interactions, but could also serve as a starting point for high-throughput assay systems and new protein detection technologies (5-7).…”

mentioning

confidence: 99%

Structural and functional analysis of phosphorylation-specific binders of the kinase ERK from designed ankyrin repeat protein libraries

Kummer

Parizek

Rube

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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We have selected designed ankyrin repeat proteins (DARPins) from a synthetic library by using ribosome display that selectively bind to the mitogen-activated protein kinase ERK2 (extracellular signal-regulated kinase 2) in either its nonphosphorylated (inactive) or doubly phosphorylated (active) form. They do not bind to other kinases tested. Crystal structures of complexes with two DARPins, each specific for one of the kinase forms, were obtained. The two DARPins bind to essentially the same region of the kinase, but recognize the conformational change within the activation loop and an adjacent area, which is the key structural difference that occurs upon activation. Whereas the rigid phosphorylated activation loop remains in the same form when bound by the DARPin, the more mobile unphosphorylated loop is pushed to a new position. The DARPins can be used to selectively precipitate the cognate form of the kinases from cell lysates. They can also specifically recognize the modification status of the kinase inside the cell. By fusing the kinase with Renilla luciferase and the DARPin to GFP, an energy transfer from luciferase to GFP can be observed in COS-7 cells upon intracellular complex formation. Phosphorylated ERK2 is seen to increase by incubation of the COS-7 cells with FBS and to decrease upon adding the ERK pathway inhibitor PD98509. Furthermore, the anti-ERK2 DARPin is seen to inhibit ERK phosphorylation as it blocks the target inside the cell. This strategy of creating activation-state-specific sensors and kinase-specific inhibitors may add to the repertoire to investigate intracellular signaling in real time.intrabodies | X-ray crystallography

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“…The antibody-based and fluorescent tag methods are therefore complementary for large scale studies of protein localization in cellular systems. The reason that no one, so far, has attempted to use the antibody approach in large scale is most likely the lack of protein binders to an adequate number of proteins (6). The Swedish Human Protein Atlas (HPA) 1 program has recently been set up to allow for systematic exploration of the human proteome using antibody-based proteomics (7).…”

Section: Molecular and Cellular Proteomics 7:499 -508 2008mentioning

confidence: 99%

Toward a Confocal Subcellular Atlas of the Human Proteome

Barbe

Lundberg

Oksvold

et al. 2008

Molecular & Cellular Proteomics

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129

112

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Information on protein localization on the subcellular level is important to map and characterize the proteome and to better understand cellular functions of proteins. Here we report on a pilot study of 466 proteins in three human cell lines aimed to allow large scale confocal microscopy analysis using protein-specific antibodies. Approximately 3000 high resolution images were generated, and more than 80% of the analyzed proteins could be classified in one or multiple subcellular compartment(s). The localizations of the proteins showed, in many cases, good agreement with the Gene Ontology localization prediction model. This is the first large scale antibody-based study to localize proteins into subcellular compartments using antibodies and confocal microscopy. The results suggest that this approach might be a valuable tool in conjunction with predictive models for protein localization.

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ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome

Abstract: International audienc

Cited by 220 publications

References 38 publications

A Genecentric Human Protein Atlas for Expression Profiles Based on Antibodies

A Genecentric Human Protein Atlas for Expression Profiles Based on Antibodies

Structural and functional analysis of phosphorylation-specific binders of the kinase ERK from designed ankyrin repeat protein libraries

Toward a Confocal Subcellular Atlas of the Human Proteome

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