Literature DB >> 26436480

A strategy for dissecting the architectures of native macromolecular assemblies.

Yi Shi1, Riccardo Pellarin2,3,4,5, Peter C Fridy6, Javier Fernandez-Martinez6, Mary K Thompson6, Yinyin Li1, Qing Jun Wang, Andrej Sali2,3,4, Michael P Rout6, Brian T Chait1.   

Abstract

It remains particularly problematic to define the structures of native macromolecular assemblies, which are often of low abundance. Here we present a strategy for isolating complexes at endogenous levels from GFP-tagged transgenic cell lines. Using cross-linking mass spectrometry, we extracted distance restraints that allowed us to model the complexes' molecular architectures.

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Year:  2015        PMID： 26436480      PMCID： PMC4803312          DOI： 10.1038/nmeth.3617

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  52 in total

1.  Molecular architecture and function of the SEA complex, a modulator of the TORC1 pathway.

Authors:  Romain Algret; Javier Fernandez-Martinez; Yi Shi; Seung Joong Kim; Riccardo Pellarin; Peter Cimermancic; Emilie Cochet; Andrej Sali; Brian T Chait; Michael P Rout; Svetlana Dokudovskaya
Journal:  Mol Cell Proteomics       Date:  2014-07-29       Impact factor: 5.911

2.  Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex.

Authors:  Yi Shi; Javier Fernandez-Martinez; Elina Tjioe; Riccardo Pellarin; Seung Joong Kim; Rosemary Williams; Dina Schneidman-Duhovny; Andrej Sali; Michael P Rout; Brian T Chait
Journal:  Mol Cell Proteomics       Date:  2014-08-26       Impact factor: 5.911

3.  See & Catch method for studying protein complexes in yeast cells: a technique unifying fluorescence microscopy and mass spectrometry.

Authors:  Changhui Deng; Andrew N Krutchinsky
Journal:  Methods Mol Biol       Date:  2014

Review 4.  Targeting autophagy in neurodegenerative diseases.

Authors:  René L Vidal; Soledad Matus; Leslie Bargsted; Claudio Hetz
Journal:  Trends Pharmacol Sci       Date:  2014-09-27       Impact factor: 14.819

5.  Nrbf2 protein suppresses autophagy by modulating Atg14L protein-containing Beclin 1-Vps34 complex architecture and reducing intracellular phosphatidylinositol-3 phosphate levels.

Authors:  Yu Zhong; Deanna H Morris; Lin Jin; Mittul S Patel; Senthil K Karunakaran; You-Jun Fu; Emily A Matuszak; Heidi L Weiss; Brian T Chait; Qing Jun Wang
Journal:  J Biol Chem       Date:  2014-08-01       Impact factor: 5.157

6.  Molecular architecture and mechanism of the anaphase-promoting complex.

Authors:  Lei-Fu Chang; Ziguo Zhang; Jing Yang; Stephen H McLaughlin; David Barford
Journal:  Nature       Date:  2014-07-20       Impact factor: 49.962

7.  eIF2B is a decameric guanine nucleotide exchange factor with a γ2ε2 tetrameric core.

Authors:  Yuliya Gordiyenko; Carla Schmidt; Martin D Jennings; Dijana Matak-Vinkovic; Graham D Pavitt; Carol V Robinson
Journal:  Nat Commun       Date:  2014-05-23       Impact factor: 14.919

8.  Architecture of the Saccharomyces cerevisiae RNA polymerase I Core Factor complex.

Authors:  Bruce A Knutson; Jie Luo; Jeffrey Ranish; Steven Hahn
Journal:  Nat Struct Mol Biol       Date:  2014-08-17       Impact factor: 15.369

9.  A robust pipeline for rapid production of versatile nanobody repertoires.

Authors:  Peter C Fridy; Yinyin Li; Sarah Keegan; Mary K Thompson; Ilona Nudelman; Johannes F Scheid; Marlene Oeffinger; Michel C Nussenzweig; David Fenyö; Brian T Chait; Michael P Rout
Journal:  Nat Methods       Date:  2014-11-02       Impact factor: 28.547

10.  Molecular architecture of the 40S⋅eIF1⋅eIF3 translation initiation complex.

Authors:  Jan P Erzberger; Florian Stengel; Riccardo Pellarin; Suyang Zhang; Tanja Schaefer; Christopher H S Aylett; Peter Cimermančič; Daniel Boehringer; Andrej Sali; Ruedi Aebersold; Nenad Ban
Journal:  Cell       Date:  2014-08-28       Impact factor: 41.582
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  67 in total

1.  Cross-linking immunoprecipitation-MS (xIP-MS): Topological Analysis of Chromatin-associated Protein Complexes Using Single Affinity Purification.

Authors:  Matthew M Makowski; Esther Willems; Pascal W T C Jansen; Michiel Vermeulen
Journal:  Mol Cell Proteomics       Date:  2015-11-11       Impact factor: 5.911

Review 2.  Apical control of conidiation in Aspergillus nidulans.

Authors:  Elixabet Oiartzabal-Arano; Elixabet Perez-de-Nanclares-Arregi; Eduardo A Espeso; Oier Etxebeste
Journal:  Curr Genet       Date:  2016-01-18       Impact factor: 3.886

3.  Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling.

Authors:  Massimiliano Bonomi; Samuel Hanot; Charles H Greenberg; Andrej Sali; Michael Nilges; Michele Vendruscolo; Riccardo Pellarin
Journal:  Structure       Date:  2018-11-01       Impact factor: 5.006

Review 4.  Chemical cross-linking in the structural analysis of protein assemblies.

Authors:  Feixia Chu; Daniel T Thornton; Hieu T Nguyen
Journal:  Methods       Date:  2018-05-30       Impact factor: 3.608

5.  Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules.

Authors:  Brinda Vallat; Benjamin Webb; John D Westbrook; Andrej Sali; Helen M Berman
Journal:  Structure       Date:  2018-04-12       Impact factor: 5.006

6.  Targeting the nuclear RNA exosome: Poly(A) binding proteins enter the stage.

Authors:  Nicola Meola; Torben Heick Jensen
Journal:  RNA Biol       Date:  2017-04-19       Impact factor: 4.652

7.  Mass spectrometry-based cross-linking study shows that the Psb28 protein binds to cytochrome b559 in Photosystem II.

Authors:  Daniel A Weisz; Haijun Liu; Hao Zhang; Sundarapandian Thangapandian; Emad Tajkhorshid; Michael L Gross; Himadri B Pakrasi
Journal:  Proc Natl Acad Sci U S A       Date:  2017-02-13       Impact factor: 11.205

8.  Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities.

Authors:  Marinka Zitnik; Francis Nguyen; Bo Wang; Jure Leskovec; Anna Goldenberg; Michael M Hoffman
Journal:  Inf Fusion       Date:  2018-09-21       Impact factor: 12.975

9.  Intracellular displacement of p53 using transactivation domain (p53 TAD) specific nanobodies.

Authors:  Anneleen Steels; Adriaan Verhelle; Olivier Zwaenepoel; Jan Gettemans
Journal:  MAbs       Date:  2018-09-11       Impact factor: 5.857

10.  Trifunctional cross-linker for mapping protein-protein interaction networks and comparing protein conformational states.

Authors:  Dan Tan; Qiang Li; Mei-Jun Zhang; Chao Liu; Chengying Ma; Pan Zhang; Yue-He Ding; Sheng-Bo Fan; Li Tao; Bing Yang; Xiangke Li; Shoucai Ma; Junjie Liu; Boya Feng; Xiaohui Liu; Hong-Wei Wang; Si-Min He; Ning Gao; Keqiong Ye; Meng-Qiu Dong; Xiaoguang Lei
Journal:  Elife       Date:  2016-03-08       Impact factor: 8.140
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