Literature DB >> 29218563

A Practical Guide to iSPOT Modeling: An Integrative Structural Biology Platform.

An Hsieh1, Lanyuan Lu2, Mark R Chance1, Sichun Yang3.   

Abstract

Integrative structure modeling is an emerging method for structural determination of protein-protein complexes that are challenging for conventional structural techniques. Here, we provide a practical protocol for implementing our integrated iSPOT platform by integrating three different biophysical techniques: small-angle X-ray scattering (SAXS), hydroxyl radical footprinting, and computational docking simulations. Specifically, individual techniques are described from experimental and/or computational perspectives, and complementary structural information from these different techniques are integrated for accurate characterization of the structures of large protein-protein complexes.

Keywords:  Computational docking simulation; Hydroxyl radical footprinting; Integrative structural biology; Protein-protein interaction; SAXS; Structural mass spectrometry; iSPOT

Mesh:

Substances:

Year:  2017        PMID: 29218563     DOI: 10.1007/978-981-10-6038-0_14

Source DB:  PubMed          Journal:  Adv Exp Med Biol        ISSN: 0065-2598            Impact factor:   2.622


  8 in total

Review 1.  Principles for Integrative Structural Biology Studies.

Authors:  Michael P Rout; Andrej Sali
Journal:  Cell       Date:  2019-05-30       Impact factor: 41.582

2.  A Metastable Contact and Structural Disorder in the Estrogen Receptor Transactivation Domain.

Authors:  Yi Peng; Shufen Cao; Janna Kiselar; Xiangzhu Xiao; Zhanwen Du; An Hsieh; Soobin Ko; Yinghua Chen; Prashansa Agrawal; Wenwei Zheng; Wuxian Shi; Wei Jiang; Lin Yang; Mark R Chance; Witold K Surewicz; Matthias Buck; Sichun Yang
Journal:  Structure       Date:  2018-12-20       Impact factor: 5.006

3.  Integration of software tools for integrative modeling of biomolecular systems.

Authors:  Matthew Hancock; Thomas-Otavio Peulen; Benjamin Webb; Billy Poon; James S Fraser; Paul Adams; Andrej Sali
Journal:  J Struct Biol       Date:  2022-02-09       Impact factor: 3.234

Review 4.  Protein Footprinting: Auxiliary Engine to Power the Structural Biology Revolution.

Authors:  Mark R Chance; Erik R Farquhar; Sichun Yang; David T Lodowski; Janna Kiselar
Journal:  J Mol Biol       Date:  2020-02-21       Impact factor: 5.469

Review 5.  From integrative structural biology to cell biology.

Authors:  Andrej Sali
Journal:  J Biol Chem       Date:  2021-05-03       Impact factor: 5.157

6.  Archiving and disseminating integrative structure models.

Authors:  Brinda Vallat; Benjamin Webb; John Westbrook; Andrej Sali; Helen M Berman
Journal:  J Biomol NMR       Date:  2019-07-05       Impact factor: 2.835

7.  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

8.  Multidomain architecture of estrogen receptor reveals interfacial cross-talk between its DNA-binding and ligand-binding domains.

Authors:  Wei Huang; Yi Peng; Janna Kiselar; Xuan Zhao; Aljawharah Albaqami; Daniel Mendez; Yinghua Chen; Srinivas Chakravarthy; Sayan Gupta; Corie Ralston; Hung-Ying Kao; Mark R Chance; Sichun Yang
Journal:  Nat Commun       Date:  2018-08-30       Impact factor: 14.919

  8 in total

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