Literature DB >> 23503679

Protein interaction discovery using parallel analysis of translated ORFs (PLATO).

Jian Zhu1,2,3, H Benjamin Larman1,4,5,2,3, Geng Gao1,2,3, Romel Somwar6, Zijuan Zhang7, Uri Laserson4,2,8, Alberto Ciccia1,2,3, Natalya Pavlova1,2,3, George Church4,2, Wei Zhang7, Santosh Kesari9, Stephen J Elledge1,2,3.   

Abstract

Identifying physical interactions between proteins and other molecules is a critical aspect of biological analysis. Here we describe PLATO, an in vitro method for mapping such interactions by affinity enrichment of a library of full-length open reading frames displayed on ribosomes, followed by massively parallel analysis using DNA sequencing. We demonstrate the broad utility of the method for human proteins by identifying known and previously unidentified interacting partners of LYN kinase, patient autoantibodies, and the small-molecules gefitinib and dasatinib.

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Year:  2013        PMID: 23503679      PMCID: PMC4110636          DOI: 10.1038/nbt.2539

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN: 1087-0156            Impact factor:   54.908


  13 in total

Review 1.  Proteomics.

Authors:  Heng Zhu; Metin Bilgin; Michael Snyder
Journal:  Annu Rev Biochem       Date:  2003       Impact factor: 23.643

2.  Phage display of cDNA libraries: enrichment of cDNA expression using open reading frame selection.

Authors:  Peggy Ho Faix; Michael A Burg; Michelle Gonzales; Edward P Ravey; Andrew Baird; David Larocca
Journal:  Biotechniques       Date:  2004-06       Impact factor: 1.993

3.  Cellular targets of gefitinib.

Authors:  Dirk Brehmer; Zoltán Greff; Klaus Godl; Stephanie Blencke; Alexander Kurtenbach; Martina Weber; Stefan Müller; Bert Klebl; Matt Cotten; György Kéri; Josef Wissing; Henrik Daub
Journal:  Cancer Res       Date:  2005-01-15       Impact factor: 12.701

Review 4.  Structure and regulation of Src family kinases.

Authors:  Titus J Boggon; Michael J Eck
Journal:  Oncogene       Date:  2004-10-18       Impact factor: 9.867

5.  Liar, a novel Lyn-binding nuclear/cytoplasmic shuttling protein that influences erythropoietin-induced differentiation.

Authors:  Amy L Samuels; S Peter Klinken; Evan Ingley
Journal:  Blood       Date:  2008-12-08       Impact factor: 22.113

6.  Identification of Src, Fyn, and Lyn SH3-binding proteins: implications for a function of SH3 domains.

Authors:  Z Weng; S M Thomas; R J Rickles; J A Taylor; A W Brauer; C Seidel-Dugan; W M Michael; G Dreyfuss; J S Brugge
Journal:  Mol Cell Biol       Date:  1994-07       Impact factor: 4.272

7.  Rapid identification of monospecific monoclonal antibodies using a human proteome microarray.

Authors:  Jun Seop Jeong; Lizhi Jiang; Edisa Albino; Josean Marrero; Hee Sool Rho; Jianfei Hu; Shaohui Hu; Carlos Vera; Diane Bayron-Poueymiroy; Zully Ann Rivera-Pacheco; Leonardo Ramos; Cecil Torres-Castro; Jiang Qian; Joseph Bonaventura; Jef D Boeke; Wendy Y Yap; Ignacio Pino; Daniel J Eichinger; Heng Zhu; Seth Blackshaw
Journal:  Mol Cell Proteomics       Date:  2012-02-03       Impact factor: 5.911

8.  hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes.

Authors:  Philippe Lamesch; Ning Li; Stuart Milstein; Changyu Fan; Tong Hao; Gabor Szabo; Zhenjun Hu; Kavitha Venkatesan; Graeme Bethel; Paul Martin; Jane Rogers; Stephanie Lawlor; Stuart McLaren; Amélie Dricot; Heather Borick; Michael E Cusick; Jean Vandenhaute; Ian Dunham; David E Hill; Marc Vidal
Journal:  Genomics       Date:  2007-01-05       Impact factor: 5.736

9.  Human TRIM gene expression in response to interferons.

Authors:  Laetitia Carthagena; Anna Bergamaschi; Joseph M Luna; Annie David; Pradeep D Uchil; Florence Margottin-Goguet; Walther Mothes; Uriel Hazan; Catherine Transy; Gianfranco Pancino; Sébastien Nisole
Journal:  PLoS One       Date:  2009-03-17       Impact factor: 3.240

10.  Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.

Authors:  Da Wei Huang; Brad T Sherman; Richard A Lempicki
Journal:  Nucleic Acids Res       Date:  2008-11-25       Impact factor: 16.971

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  25 in total

1.  Viral immunology. Comprehensive serological profiling of human populations using a synthetic human virome.

Authors:  George J Xu; Tomasz Kula; Qikai Xu; Mamie Z Li; Suzanne D Vernon; Thumbi Ndung'u; Kiat Ruxrungtham; Jorge Sanchez; Christian Brander; Raymond T Chung; Kevin C O'Connor; Bruce Walker; H Benjamin Larman; Stephen J Elledge
Journal:  Science       Date:  2015-06-05       Impact factor: 47.728

2.  Brief Report: Anti-RNPC-3 Antibodies As a Marker of Cancer-Associated Scleroderma.

Authors:  Ami A Shah; George Xu; Antony Rosen; Laura K Hummers; Fredrick M Wigley; Stephen J Elledge; Livia Casciola-Rosen
Journal:  Arthritis Rheumatol       Date:  2017-06       Impact factor: 10.995

3.  Multiplex single-molecule interaction profiling of DNA-barcoded proteins.

Authors:  Liangcai Gu; Chao Li; John Aach; David E Hill; Marc Vidal; George M Church
Journal:  Nature       Date:  2014-09-21       Impact factor: 49.962

4.  High-resolution antibody dynamics of vaccine-induced immune responses.

Authors:  Uri Laserson; Francois Vigneault; Daniel Gadala-Maria; Gur Yaari; Mohamed Uduman; Jason A Vander Heiden; William Kelton; Sang Taek Jung; Yi Liu; Jonathan Laserson; Raj Chari; Je-Hyuk Lee; Ido Bachelet; Brendan Hickey; Erez Lieberman-Aiden; Bozena Hanczaruk; Birgitte B Simen; Michael Egholm; Daphne Koller; George Georgiou; Steven H Kleinstein; George M Church
Journal:  Proc Natl Acad Sci U S A       Date:  2014-03-17       Impact factor: 11.205

5.  SORTCERY-A High-Throughput Method to Affinity Rank Peptide Ligands.

Authors:  Lothar Luther Reich; Sanjib Dutta; Amy E Keating
Journal:  J Mol Biol       Date:  2014-10-12       Impact factor: 5.469

6.  Crosslinking of DNA-linked ligands to target proteins for enrichment from DNA-encoded libraries.

Authors:  Kyle E Denton; Casey J Krusemark
Journal:  Medchemcomm       Date:  2016-08-02       Impact factor: 3.597

Review 7.  A tale of two approaches: how metagenomics and proteomics are shaping the future of encephalitis diagnostics.

Authors:  Ryan D Schubert; Michael R Wilson
Journal:  Curr Opin Neurol       Date:  2015-06       Impact factor: 5.710

8.  Association study between copy number variation and beef fatty acid profile of Nellore cattle.

Authors:  Marcos Vinicius Antunes de Lemos; Elisa Peripolli; Mariana Piatto Berton; Fabiele Loise Braga Feitosa; Bianca Ferreira Olivieri; Nedenia Bonvino Stafuzza; Rafael Lara Tonussi; Sabrina Kluska; Hermenegildo Lucas Justino Chiaia; Lenise Mueller; Adrielli Mathias Ferrinho; Angelica Simone Cravo Prereira; Henrique Nunes de Oliveira; Lucia Galvão de Albuquerque; Fernando Baldi
Journal:  J Appl Genet       Date:  2018-03-08       Impact factor: 3.240

9.  Systematic autoantigen analysis identifies a distinct subtype of scleroderma with coincident cancer.

Authors:  George J Xu; Ami A Shah; Mamie Z Li; Qikai Xu; Antony Rosen; Livia Casciola-Rosen; Stephen J Elledge
Journal:  Proc Natl Acad Sci U S A       Date:  2016-11-07       Impact factor: 11.205

10.  Generating High-Accuracy Peptide-Binding Data in High Throughput with Yeast Surface Display and SORTCERY.

Authors:  Lothar Luther Reich; Sanjib Dutta; Amy E Keating
Journal:  Methods Mol Biol       Date:  2016
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