Literature DB >> 20507923

Integrative structure modeling of macromolecular assemblies from proteomics data.

Keren Lasker1, Jeremy L Phillips, Daniel Russel, Javier Velázquez-Muriel, Dina Schneidman-Duhovny, Elina Tjioe, Ben Webb, Avner Schlessinger, Andrej Sali.   

Abstract

Proteomics techniques have been used to generate comprehensive lists of protein interactions in a number of species. However, relatively little is known about how these interactions result in functional multiprotein complexes. This gap can be bridged by combining data from proteomics experiments with data from established structure determination techniques. Correspondingly, integrative computational methods are being developed to provide descriptions of protein complexes at varying levels of accuracy and resolution, ranging from complex compositions to detailed atomic structures.

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Year:  2010        PMID: 20507923      PMCID: PMC2938050          DOI: 10.1074/mcp.R110.000067

Source DB:  PubMed          Journal:  Mol Cell Proteomics        ISSN: 1535-9476            Impact factor:   5.911


  138 in total

1.  A protein-protein interaction map of yeast RNA polymerase III.

Authors:  A Flores; J F Briand; O Gadal; J C Andrau; L Rubbi; V Van Mullem; C Boschiero; M Goussot; C Marck; C Carles; P Thuriaux; A Sentenac; M Werner
Journal:  Proc Natl Acad Sci U S A       Date:  1999-07-06       Impact factor: 11.205

2.  De novo protein structure determination using sparse NMR data.

Authors:  P M Bowers; C E Strauss; D Baker
Journal:  J Biomol NMR       Date:  2000-12       Impact factor: 2.835

3.  Dissociable Rpb4-Rpb7 subassembly of rna polymerase II binds to single-strand nucleic acid and mediates a post-recruitment step in transcription initiation.

Authors:  S M Orlicky; P T Tran; M H Sayre; A M Edwards
Journal:  J Biol Chem       Date:  2000-11-21       Impact factor: 5.157

Review 4.  Structural symmetry and protein function.

Authors:  D S Goodsell; A J Olson
Journal:  Annu Rev Biophys Biomol Struct       Date:  2000

5.  Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins.

Authors:  K T Simons; I Ruczinski; C Kooperberg; B A Fox; C Bystroff; D Baker
Journal:  Proteins       Date:  1999-01-01

6.  A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae.

Authors:  P Uetz; L Giot; G Cagney; T A Mansfield; R S Judson; J R Knight; D Lockshon; V Narayan; M Srinivasan; P Pochart; A Qureshi-Emili; Y Li; B Godwin; D Conover; T Kalbfleisch; G Vijayadamodar; M Yang; M Johnston; S Fields; J M Rothberg
Journal:  Nature       Date:  2000-02-10       Impact factor: 49.962

7.  Protein interaction mapping in C. elegans using proteins involved in vulval development.

Authors:  A J Walhout; R Sordella; X Lu; J L Hartley; G F Temple; M A Brasch; N Thierry-Mieg; M Vidal
Journal:  Science       Date:  2000-01-07       Impact factor: 47.728

8.  The Saccharomyces telomere-binding protein Cdc13p interacts with both the catalytic subunit of DNA polymerase alpha and the telomerase-associated est1 protein.

Authors:  H Qi; V A Zakian
Journal:  Genes Dev       Date:  2000-07-15       Impact factor: 11.361

9.  High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry.

Authors:  M M Young; N Tang; J C Hempel; C M Oshiro; E W Taylor; I D Kuntz; B W Gibson; G Dollinger
Journal:  Proc Natl Acad Sci U S A       Date:  2000-05-23       Impact factor: 11.205

Review 10.  New frontiers in gold labeling.

Authors:  J F Hainfeld; R D Powell
Journal:  J Histochem Cytochem       Date:  2000-04       Impact factor: 2.479

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  37 in total

1.  Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach.

Authors:  Keren Lasker; Friedrich Förster; Stefan Bohn; Thomas Walzthoeni; Elizabeth Villa; Pia Unverdorben; Florian Beck; Ruedi Aebersold; Andrej Sali; Wolfgang Baumeister
Journal:  Proc Natl Acad Sci U S A       Date:  2012-01-23       Impact factor: 11.205

2.  Toward an integrated structural model of the 26S proteasome.

Authors:  Friedrich Förster; Keren Lasker; Stephan Nickell; Andrej Sali; Wolfgang Baumeister
Journal:  Mol Cell Proteomics       Date:  2010-05-13       Impact factor: 5.911

3.  Computational tools for the interactive exploration of proteomic and structural data.

Authors:  John H Morris; Elaine C Meng; Thomas E Ferrin
Journal:  Mol Cell Proteomics       Date:  2010-06-04       Impact factor: 5.911

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.  A critical assessment of information-guided protein-protein docking predictions.

Authors:  Edward S C Shih; Ming-Jing Hwang
Journal:  Mol Cell Proteomics       Date:  2012-12-13       Impact factor: 5.911

6.  Bound anions differentially stabilize multiprotein complexes in the absence of bulk solvent.

Authors:  Linjie Han; Suk-Joon Hyung; Jonathan J S Mayers; Brandon T Ruotolo
Journal:  J Am Chem Soc       Date:  2011-06-30       Impact factor: 15.419

7.  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

8.  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

9.  Modeling protein assemblies in the proteome.

Authors:  Guray Kuzu; Ozlem Keskin; Ruth Nussinov; Attila Gursoy
Journal:  Mol Cell Proteomics       Date:  2014-01-20       Impact factor: 5.911

Review 10.  From local structure to a global framework: recognition of protein folds.

Authors:  Agnel Praveen Joseph; Alexandre G de Brevern
Journal:  J R Soc Interface       Date:  2014-04-16       Impact factor: 4.118

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