메뉴 건너뛰기




Volumn 12, Issue 8, 2015, Pages 787-793

Quantifying domain-ligand affinities and specificities by high-throughput holdup assay

Author keywords

[No Author keywords available]

Indexed keywords

AVIDIN; CELL PROTEIN; LIGAND; ONCOPROTEIN; PDZ PROTEIN; RESIN; DNA BINDING PROTEIN; E6 PROTEIN, HUMAN PAPILLOMAVIRUS TYPE 16; E6 PROTEIN, HUMAN PAPILLOMAVIRUS TYPE 18; PROTEIN; PROTEOME; REPRESSOR PROTEIN;

EID: 84938423622     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.3438     Document Type: Article
Times cited : (65)

References (44)
  • 1
    • 84864584758 scopus 로고    scopus 로고
    • Why modules matter
    • Nash, P.D. Why modules matter. FEBS Lett. 586, 2572-2574 (2012).
    • (2012) FEBS Lett , vol.586 , pp. 2572-2574
    • Nash, P.D.1
  • 2
    • 49549122501 scopus 로고    scopus 로고
    • Understanding eukaryotic linear motifs and their role in cell signaling and regulation
    • Diella, F. et al. Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Front. Biosci. 13, 6580-6603 (2008).
    • (2008) Front. Biosci , vol.13 , pp. 6580-6603
    • Diella, F.1
  • 3
    • 77958549006 scopus 로고    scopus 로고
    • Large-scale protein interactome mapping: Strategies and opportunities
    • Lievens, S., Eyckerman, S., Lemmens, I. & Tavernier, J. Large-scale protein interactome mapping: strategies and opportunities. Expert Rev. Proteomics 7, 679-690 (2010).
    • (2010) Expert Rev. Proteomics , vol.7 , pp. 679-690
    • Lievens, S.1    Eyckerman, S.2    Lemmens, I.3    Tavernier, J.4
  • 4
    • 70350404403 scopus 로고    scopus 로고
    • Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins
    • Tonikian, R. et al. Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins. PLoS Biol. 7, e1000218 (2009).
    • (2009) PLoS Biol , vol.7 , pp. e1000218
    • Tonikian, R.1
  • 5
    • 84864577164 scopus 로고    scopus 로고
    • The application of modular protein domains in proteomics
    • Jadwin, J.A., Ogiue-Ikeda, M. & Machida, K. The application of modular protein domains in proteomics. FEBS Lett. 586, 2586-2596 (2012).
    • (2012) FEBS Lett , vol.586 , pp. 2586-2596
    • Jadwin, J.A.1    Ogiue-Ikeda, M.2    Machida, K.3
  • 6
    • 0030604722 scopus 로고    scopus 로고
    • Crystal structures of a complexed and peptide-free membrane protein-binding domain: Molecular basis of peptide recognition by PDZ
    • Doyle, D.A. et al. Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ. Cell 85, 1067-1076 (1996).
    • (1996) Cell , vol.85 , pp. 1067-1076
    • Doyle, D.A.1
  • 7
    • 84864590078 scopus 로고    scopus 로고
    • The emerging contribution of sequence context to the specificity of protein interactions mediated by PDZ domains
    • Luck, K., Charbonnier, S. & Trav, G. The emerging contribution of sequence context to the specificity of protein interactions mediated by PDZ domains. FEBS Lett. 586, 2648-2661 (2012).
    • (2012) FEBS Lett , vol.586 , pp. 2648-2661
    • Luck, K.1    Charbonnier, S.2    Trav, G.3
  • 8
    • 0012927828 scopus 로고    scopus 로고
    • PDZ domain proteins: Plug and play!
    • RE7
    • Nourry, C., Grant, S.G. & Borg, J.P. PDZ domain proteins: plug and play! Sci. STKE 2003, RE7 (2003).
    • (2003) Sci. STKE , vol.2003
    • Nourry, C.1    Grant, S.G.2    Borg, J.P.3
  • 9
    • 54549104845 scopus 로고    scopus 로고
    • Crosstalk between small GTPases and polarity proteins in cell polarization
    • Iden, S. & Collard, J.G. Crosstalk between small GTPases and polarity proteins in cell polarization. Nat. Rev. Mol. Cell Biol. 9, 846-859 (2008).
    • (2008) Nat. Rev. Mol. Cell Biol , vol.9 , pp. 846-859
    • Iden, S.1    Collard, J.G.2
  • 10
    • 80655143495 scopus 로고    scopus 로고
    • Emerging theme: Cellular PDZ proteins as common targets of pathogenic viruses
    • Javier, R.T. & Rice, A.P. Emerging theme: cellular PDZ proteins as common targets of pathogenic viruses. J. Virol. 85, 11544-11556 (2011).
    • (2011) J. Virol , vol.85 , pp. 11544-11556
    • Javier, R.T.1    Rice, A.P.2
  • 11
    • 33750448672 scopus 로고    scopus 로고
    • Capturing protein-protein complexes at equilibrium: The holdup comparative chromatographic retention assay
    • Charbonnier, S., Zanier, K., Masson, M. & Trav, G. Capturing protein-protein complexes at equilibrium: the holdup comparative chromatographic retention assay. Protein Expr. Purif. 50, 89-101 (2006).
    • (2006) Protein Expr. Purif , vol.50 , pp. 89-101
    • Charbonnier, S.1    Zanier, K.2    Masson, M.3    Trav, G.4
  • 12
    • 84858197572 scopus 로고    scopus 로고
    • Putting into practice domain-linear motif interaction predictions for exploration of protein networks
    • Luck, K. et al. Putting into practice domain-linear motif interaction predictions for exploration of protein networks. PLoS ONE 6, e25376 (2011).
    • (2011) PLoS ONE , vol.6 , pp. e25376
    • Luck, K.1
  • 13
    • 34547127612 scopus 로고    scopus 로고
    • PDZ domain binding selectivity is optimized across the mouse proteome
    • Stiffler, M.A. et al. PDZ domain binding selectivity is optimized across the mouse proteome. Science 317, 364-369 (2007).
    • (2007) Science , vol.317 , pp. 364-369
    • Stiffler, M.A.1
  • 14
    • 78951488641 scopus 로고    scopus 로고
    • A systematic analysis of human papillomavirus (HPV) E6 PDZ substrates identifies MAGI-1 as a major target of HPV type 16 (HPV-16) and HPV-18 whose loss accompanies disruption of tight junctions
    • Kranjec, C. & Banks, L. A systematic analysis of human papillomavirus (HPV) E6 PDZ substrates identifies MAGI-1 as a major target of HPV type 16 (HPV-16) and HPV-18 whose loss accompanies disruption of tight junctions. J. Virol. 85, 1757-1764 (2011).
    • (2011) J. Virol , vol.85 , pp. 1757-1764
    • Kranjec, C.1    Banks, L.2
  • 15
    • 84859418077 scopus 로고    scopus 로고
    • Solution structure analysis of the HPV16 E6 oncoprotein reveals a self-association mechanism required for E6-mediated degradation of p53
    • Zanier, K. et al. Solution structure analysis of the HPV16 E6 oncoprotein reveals a self-association mechanism required for E6-mediated degradation of p53. Structure 20, 604-617 (2012).
    • (2012) Structure , vol.20 , pp. 604-617
    • Zanier, K.1
  • 17
    • 84884398431 scopus 로고    scopus 로고
    • The human PDZome: A gateway to PDZ mediated functions
    • Belotti, E. et al. The human PDZome: a gateway to PDZ mediated functions. Mol. Cell. Proteomics 12, 2587-2603 (2013).
    • (2013) Mol. Cell. Proteomics , vol.12 , pp. 2587-2603
    • Belotti, E.1
  • 18
    • 82355163586 scopus 로고    scopus 로고
    • Benchmarking a luciferase complementation assay for detecting protein complexes
    • Cassonnet, P. et al. Benchmarking a luciferase complementation assay for detecting protein complexes. Nat. Methods 8, 990-992 (2011).
    • (2011) Nat. Methods , vol.8 , pp. 990-992
    • Cassonnet, P.1
  • 19
    • 77249119762 scopus 로고    scopus 로고
    • The landscape of somatic copy-number alteration across human cancers
    • Beroukhim, R. et al. The landscape of somatic copy-number alteration across human cancers. Nature 463, 899-905 (2010).
    • (2010) Nature , vol.463 , pp. 899-905
    • Beroukhim, R.1
  • 20
    • 84855344423 scopus 로고    scopus 로고
    • Identification of MAGI1 as a tumor-suppressor protein induced by cyclooxygenase-2 inhibitors in colorectal cancer cells
    • Zaric, J. et al. Identification of MAGI1 as a tumor-suppressor protein induced by cyclooxygenase-2 inhibitors in colorectal cancer cells. Oncogene 31, 48-59 (2012).
    • (2012) Oncogene , vol.31 , pp. 48-59
    • Zaric, J.1
  • 21
    • 79952292419 scopus 로고    scopus 로고
    • MAGI-3 competes with NHERF-2 to negatively regulate LPA2 receptor signaling in colon cancer cells
    • Lee, S.J. et al. MAGI-3 competes with NHERF-2 to negatively regulate LPA2 receptor signaling in colon cancer cells. Gastroenterology 140, 924-934 (2011).
    • (2011) Gastroenterology , vol.140 , pp. 924-934
    • Lee, S.J.1
  • 22
    • 23844473290 scopus 로고    scopus 로고
    • Binding of PTEN to specific PDZ domains contributes to PTEN protein stability and phosphorylation by microtubule-associated serine/threonine kinases
    • Valiente, M. et al. Binding of PTEN to specific PDZ domains contributes to PTEN protein stability and phosphorylation by microtubule-associated serine/threonine kinases. J. Biol. Chem. 280, 28936-28943 (2005).
    • (2005) J. Biol. Chem , vol.280 , pp. 28936-28943
    • Valiente, M.1
  • 23
    • 11244250646 scopus 로고    scopus 로고
    • Implication of the MAGI-1b/PTEN signalosome in stabilization of adherens junctions and suppression of invasiveness
    • Kotelevets, L. et al. Implication of the MAGI-1b/PTEN signalosome in stabilization of adherens junctions and suppression of invasiveness. FASEB J. 19, 115-117 (2005).
    • (2005) FASEB J , vol.19 , pp. 115-117
    • Kotelevets, L.1
  • 25
    • 84866424985 scopus 로고    scopus 로고
    • The PDZ protein discs-large (DLG): The Jekyll and Hyde of the epithelial polarity proteins
    • Roberts, S., Delury, C. & Marsh, E. The PDZ protein discs-large (DLG): the Jekyll and Hyde of the epithelial polarity proteins. FEBS J. 279, 3549-3558 (2012).
    • (2012) FEBS J , vol.279 , pp. 3549-3558
    • Roberts, S.1    Delury, C.2    Marsh, E.3
  • 26
    • 70949093176 scopus 로고    scopus 로고
    • LARG at chromosome 11q23 has functional characteristics of a tumor suppressor in human breast and colorectal cancer
    • Ong, D.C. et al. LARG at chromosome 11q23 has functional characteristics of a tumor suppressor in human breast and colorectal cancer. Oncogene 28, 4189-4200 (2009).
    • (2009) Oncogene , vol.28 , pp. 4189-4200
    • Ong, D.C.1
  • 27
    • 84920842365 scopus 로고    scopus 로고
    • PDZRN3/LNX3 is a novel target of human papillomavirus type 16 (HPV-16) and HPV-18 E6
    • Thomas, M. & Banks, L. PDZRN3/LNX3 is a novel target of human papillomavirus type 16 (HPV-16) and HPV-18 E6. J. Virol. 89, 1439-1444 (2015).
    • (2015) J. Virol , vol.89 , pp. 1439-1444
    • Thomas, M.1    Banks, L.2
  • 28
    • 12144287536 scopus 로고    scopus 로고
    • A map of WW domain family interactions
    • Hu, H. et al. A map of WW domain family interactions. Proteomics 4, 643-655 (2004).
    • (2004) Proteomics , vol.4 , pp. 643-655
    • Hu, H.1
  • 29
    • 19344377539 scopus 로고    scopus 로고
    • Protein interaction networks by proteome peptide scanning
    • Landgraf, C. et al. Protein interaction networks by proteome peptide scanning. PLoS Biol. 2, E14 (2004).
    • (2004) PLoS Biol , vol.2 , pp. E14
    • Landgraf, C.1
  • 30
    • 77954040159 scopus 로고    scopus 로고
    • Quantifying protein-protein interactions in high throughput using protein domain microarrays
    • Kaushansky, A. et al. Quantifying protein-protein interactions in high throughput using protein domain microarrays. Nat. Protoc. 5, 773-790 (2010).
    • (2010) Nat. Protoc , vol.5 , pp. 773-790
    • Kaushansky, A.1
  • 31
    • 80054062014 scopus 로고    scopus 로고
    • Peptides targeting the PDZ domain of PTPN4 are efficient inducers of glioblastoma cell death
    • Babault, N. et al. Peptides targeting the PDZ domain of PTPN4 are efficient inducers of glioblastoma cell death. Structure 19, 1518-1524 (2011).
    • (2011) Structure , vol.19 , pp. 1518-1524
    • Babault, N.1
  • 32
    • 77957771797 scopus 로고    scopus 로고
    • Transient protein-protein interactions: Structural, functional, and network properties
    • Perkins, J.R., Diboun, I., Dessailly, B.H., Lees, J.G. & Orengo, C. Transient protein-protein interactions: structural, functional, and network properties. Structure 18, 1233-1243 (2010).
    • (2010) Structure , vol.18 , pp. 1233-1243
    • Perkins, J.R.1    Diboun, I.2    Dessailly, B.H.3    Lees, J.G.4    Orengo, C.5
  • 33
    • 58149229162 scopus 로고    scopus 로고
    • An in vitro microfluidic approach to generating protein-interaction networks
    • Gerber, D., Maerkl, S.J. & Quake, S.R. An in vitro microfluidic approach to generating protein-interaction networks. Nat. Methods 6, 71-74 (2009).
    • (2009) Nat. Methods , vol.6 , pp. 71-74
    • Gerber, D.1    Maerkl, S.J.2    Quake, S.R.3
  • 34
    • 84866052943 scopus 로고    scopus 로고
    • Comprehensive binary interaction mapping of SH2 domains via fluorescence polarization reveals novel functional diversification of ErbB receptors
    • Hause, R.J. Jr. et al. Comprehensive binary interaction mapping of SH2 domains via fluorescence polarization reveals novel functional diversification of ErbB receptors. PLoS ONE 7, e44471 (2012).
    • (2012) PLoS ONE , vol.7 , pp. e44471
    • Hause, R.J.1
  • 35
    • 14744271960 scopus 로고    scopus 로고
    • ITC in the post-genomic era? Priceless
    • Velzquez Campoy, A. & Freire, E. ITC in the post-genomic era? Priceless. Biophys. Chem. 115, 115-124 (2005).
    • (2005) Biophys. Chem , vol.115 , pp. 115-124
    • Velzquez Campoy, A.1    Freire, E.2
  • 36
    • 0033955735 scopus 로고    scopus 로고
    • Advances in surface plasmon resonance biosensor analysis
    • Rich, R.L. & Myszka, D.G. Advances in surface plasmon resonance biosensor analysis. Curr. Opin. Biotechnol. 11, 54-61 (2000).
    • (2000) Curr. Opin. Biotechnol , vol.11 , pp. 54-61
    • Rich, R.L.1    Myszka, D.G.2
  • 37
    • 21244463400 scopus 로고    scopus 로고
    • SPOT synthesis: Reliability of array-based measurement of peptide binding affinity
    • Weiser, A.A. et al. SPOT synthesis: reliability of array-based measurement of peptide binding affinity. Anal. Biochem. 342, 300-311 (2005).
    • (2005) Anal. Biochem , vol.342 , pp. 300-311
    • Weiser, A.A.1
  • 38
    • 33847247484 scopus 로고    scopus 로고
    • A generic method for the production of recombinant proteins in Escherichia coli using a dual hexahistidine-maltose-binding protein affinity tag
    • Tropea, J.E., Cherry, S., Nallamsetty, S., Bignon, C. & Waugh, D.S. A generic method for the production of recombinant proteins in Escherichia coli using a dual hexahistidine-maltose-binding protein affinity tag. Methods Mol. Biol. 363, 1-19 (2007).
    • (2007) Methods Mol. Biol , vol.363 , pp. 1-19
    • Tropea, J.E.1    Cherry, S.2    Nallamsetty, S.3    Bignon, C.4    Waugh, D.S.5
  • 39
    • 0034956228 scopus 로고    scopus 로고
    • A strategy for optimizing the monodispersity of fusion proteins: Application to purification of recombinant HPV E6 oncoprotein
    • Nomin, Y. et al. A strategy for optimizing the monodispersity of fusion proteins: application to purification of recombinant HPV E6 oncoprotein. Protein Eng. 14, 297-305 (2001).
    • (2001) Protein Eng , vol.14 , pp. 297-305
    • Nomin, Y.1
  • 40
    • 80053631355 scopus 로고    scopus 로고
    • High-throughput protein expression screening and purification in Escherichia coli
    • Vincentelli, R. et al. High-throughput protein expression screening and purification in Escherichia coli. Methods 55, 65-72 (2011).
    • (2011) Methods , vol.55 , pp. 65-72
    • Vincentelli, R.1
  • 41
    • 84934435566 scopus 로고    scopus 로고
    • High-throughput expression screening and purification of recombinant proteins in E. Coli
    • Saez, N.J. & Vincentelli, R. High-throughput expression screening and purification of recombinant proteins in E. coli. Methods Mol. Biol. 1091, 33-53 (2014).
    • (2014) Methods Mol. Biol , vol.1091 , pp. 33-53
    • Saez, N.J.1    Vincentelli, R.2
  • 42
    • 79953778055 scopus 로고    scopus 로고
    • Surface plasmon resonance analysis of the binding of high-risk mucosal HPV E6 oncoproteins to the PDZ1 domain of the tight junction protein MAGI-1
    • Fournane, S. et al. Surface plasmon resonance analysis of the binding of high-risk mucosal HPV E6 oncoproteins to the PDZ1 domain of the tight junction protein MAGI-1. J. Mol. Recognit. 24, 511-523 (2011).
    • (2011) J. Mol. Recognit , vol.24 , pp. 511-523
    • Fournane, S.1
  • 43
    • 79951772229 scopus 로고    scopus 로고
    • The structural and dynamic response of MAGI-1 PDZ1 with noncanonical domain boundaries to the binding of human papillomavirus E6
    • Charbonnier, S. et al. The structural and dynamic response of MAGI-1 PDZ1 with noncanonical domain boundaries to the binding of human papillomavirus E6. J. Mol. Biol. 406, 745-763 (2011).
    • (2011) J. Mol. Biol , vol.406 , pp. 745-763
    • Charbonnier, S.1
  • 44
    • 84875490185 scopus 로고    scopus 로고
    • Cancer genome landscapes
    • Vogelstein, B. et al. Cancer genome landscapes. Science 339, 1546-1558 (2013).
    • (2013) Science , vol.339 , pp. 1546-1558
    • Vogelstein, B.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.