Literature DB >> 31150619

Principles for Integrative Structural Biology Studies.

Michael P Rout1, Andrej Sali2.   

Abstract

Integrative structure determination is a powerful approach to modeling the structures of biological systems based on data produced by multiple experimental and theoretical methods, with implications for our understanding of cellular biology and drug discovery. This Primer introduces the theory and methods of integrative approaches, emphasizing the kinds of data that can be effectively included in developing models and using the nuclear pore complex as an example to illustrate the practice and challenges involved. These guidelines are intended to aid the researcher in understanding and applying integrative structural methods to systems of their interest and thus take advantage of this rapidly evolving field. Published by Elsevier Inc.

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Year:  2019        PMID: 31150619      PMCID: PMC6810593          DOI: 10.1016/j.cell.2019.05.016

Source DB:  PubMed          Journal:  Cell        ISSN: 0092-8674            Impact factor:   41.582


  146 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

Review 2.  Fuzzy complexes: Specific binding without complete folding.

Authors:  Rashmi Sharma; Zsolt Raduly; Marton Miskei; Monika Fuxreiter
Journal:  FEBS Lett       Date:  2015-07-27       Impact factor: 4.124

Review 3.  The cargo spectrum of nuclear transport receptors.

Authors:  Imke Baade; Ralph H Kehlenbach
Journal:  Curr Opin Cell Biol       Date:  2018-12-07       Impact factor: 8.382

Review 4.  Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life.

Authors:  Anja Spang; Eva F Caceres; Thijs J G Ettema
Journal:  Science       Date:  2017-08-11       Impact factor: 47.728

5.  A toolkit and benchmark study for FRET-restrained high-precision structural modeling.

Authors:  Stanislav Kalinin; Thomas Peulen; Simon Sindbert; Paul J Rothwell; Sylvia Berger; Tobias Restle; Roger S Goody; Holger Gohlke; Claus A M Seidel
Journal:  Nat Methods       Date:  2012-11-11       Impact factor: 28.547

Review 6.  Expanding the boundaries of cryo-EM with phase plates.

Authors:  Radostin Danev; Wolfgang Baumeister
Journal:  Curr Opin Struct Biol       Date:  2017-07-01       Impact factor: 6.809

7.  Assessing the quality of solution nuclear magnetic resonance structures by complete cross-validation.

Authors:  A T Brünger; G M Clore; A M Gronenborn; R Saffrich; M Nilges
Journal:  Science       Date:  1993-07-16       Impact factor: 47.728

8.  Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography.

Authors:  Alexander Leitner; Roland Reischl; Thomas Walzthoeni; Franz Herzog; Stefan Bohn; Friedrich Förster; Ruedi Aebersold
Journal:  Mol Cell Proteomics       Date:  2012-01-27       Impact factor: 5.911

9.  Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy.

Authors:  Agnel Praveen Joseph; Ingvar Lagerstedt; Ardan Patwardhan; Maya Topf; Martyn Winn
Journal:  J Struct Biol       Date:  2017-05-25       Impact factor: 2.867

10.  Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines.

Authors:  Alessandro Ori; Niccolò Banterle; Murat Iskar; Amparo Andrés-Pons; Claudia Escher; Huy Khanh Bui; Lenore Sparks; Victor Solis-Mezarino; Oliver Rinner; Peer Bork; Edward A Lemke; Martin Beck
Journal:  Mol Syst Biol       Date:  2013       Impact factor: 11.429

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  62 in total

1.  Methods for Molecular Modelling of Protein Complexes.

Authors:  Tejashree Rajaram Kanitkar; Neeladri Sen; Sanjana Nair; Neelesh Soni; Kaustubh Amritkar; Yogendra Ramtirtha; M S Madhusudhan
Journal:  Methods Mol Biol       Date:  2021

2.  CM1-driven assembly and activation of yeast γ-tubulin small complex underlies microtubule nucleation.

Authors:  Axel F Brilot; Andrew S Lyon; Alex Zelter; Shruthi Viswanath; Alison Maxwell; Michael J MacCoss; Eric G Muller; Andrej Sali; Trisha N Davis; David A Agard
Journal:  Elife       Date:  2021-05-05       Impact factor: 8.140

3.  Structural dynamics of the human COP9 signalosome revealed by cross-linking mass spectrometry and integrative modeling.

Authors:  Craig Gutierrez; Ilan E Chemmama; Haibin Mao; Clinton Yu; Ignacia Echeverria; Sarah A Block; Scott D Rychnovsky; Ning Zheng; Andrej Sali; Lan Huang
Journal:  Proc Natl Acad Sci U S A       Date:  2020-02-07       Impact factor: 11.205

Review 4.  Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods.

Authors:  James M Krieger; Pemra Doruker; Ana Ligia Scott; David Perahia; Ivet Bahar
Journal:  Curr Opin Struct Biol       Date:  2020-07-01       Impact factor: 6.809

5.  Genetic interaction mapping informs integrative structure determination of protein complexes.

Authors:  Hannes Braberg; Ignacia Echeverria; Stefan Bohn; Peter Cimermancic; Anthony Shiver; Richard Alexander; Jiewei Xu; Michael Shales; Raghuvar Dronamraju; Shuangying Jiang; Gajendradhar Dwivedi; Derek Bogdanoff; Kaitlin K Chaung; Ruth Hüttenhain; Shuyi Wang; David Mavor; Riccardo Pellarin; Dina Schneidman; Joel S Bader; James S Fraser; John Morris; James E Haber; Brian D Strahl; Carol A Gross; Junbiao Dai; Jef D Boeke; Andrej Sali; Nevan J Krogan
Journal:  Science       Date:  2020-12-11       Impact factor: 47.728

6.  Sensitivity boosts by the CPMAS CryoProbe for challenging biological assemblies.

Authors:  Alia Hassan; Caitlin M Quinn; Jochem Struppe; Ivan V Sergeyev; Chunting Zhang; Changmiao Guo; Brent Runge; Theint Theint; Hanh H Dao; Christopher P Jaroniec; Mélanie Berbon; Alons Lends; Birgit Habenstein; Antoine Loquet; Rainer Kuemmerle; Barbara Perrone; Angela M Gronenborn; Tatyana Polenova
Journal:  J Magn Reson       Date:  2019-12-23       Impact factor: 2.229

Review 7.  Art and Science of the Cellular Mesoscale.

Authors:  David S Goodsell; Arthur J Olson; Stefano Forli
Journal:  Trends Biochem Sci       Date:  2020-03-21       Impact factor: 13.807

8.  Integrative structure and function of the yeast exocyst complex.

Authors:  Sai J Ganesan; Michael J Feyder; Ilan E Chemmama; Fei Fang; Michael P Rout; Brian T Chait; Yi Shi; Mary Munson; Andrej Sali
Journal:  Protein Sci       Date:  2020-05-01       Impact factor: 6.725

9.  Using Integrative Modeling Platform to compute, validate, and archive a model of a protein complex structure.

Authors:  Daniel J Saltzberg; Shruthi Viswanath; Ignacia Echeverria; Ilan E Chemmama; Ben Webb; Andrej Sali
Journal:  Protein Sci       Date:  2020-12-03       Impact factor: 6.725

10.  Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures.

Authors:  Helen M Berman; Paul D Adams; Alexandre A Bonvin; Stephen K Burley; Bridget Carragher; Wah Chiu; Frank DiMaio; Thomas E Ferrin; Margaret J Gabanyi; Thomas D Goddard; Patrick R Griffin; Juergen Haas; Christian A Hanke; Jeffrey C Hoch; Gerhard Hummer; Genji Kurisu; Catherine L Lawson; Alexander Leitner; John L Markley; Jens Meiler; Gaetano T Montelione; George N Phillips; Thomas Prisner; Juri Rappsilber; David C Schriemer; Torsten Schwede; Claus A M Seidel; Timothy S Strutzenberg; Dmitri I Svergun; Emad Tajkhorshid; Jill Trewhella; Brinda Vallat; Sameer Velankar; Geerten W Vuister; Benjamin Webb; John D Westbrook; Kate L White; Andrej Sali
Journal:  Structure       Date:  2019-11-25       Impact factor: 5.006

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