Literature DB >> 31054969

Single-molecule fluorescence studies of intrinsically disordered proteins and liquid phase separation.

Irem Nasir1, Paulo L Onuchic2, Sergio R Labra2, Ashok A Deniz3.   

Abstract

Intrinsically disordered proteins (IDPs) are ubiquitous in proteomes and serve in a range of cellular functions including signaling, regulation, transport and enzyme function. IDP misfunction and aggregation are also associated with several diseases including neurodegenerative diseases and cancer. During the past decade, single-molecule methods have become popular for detailed biophysical and structural studies of these complex proteins. This work has included recent applications to cellular liquid-liquid phase separation (LLPS), relevant for functional dynamics of membraneless organelles such as the nucleolus and stress granules. In this concise review, we cover the conceptual motivations for development and application of single-molecule fluorescence methods for such IDP studies. We follow with a few key examples of systems and biophysical problems that have been addressed, and conclude with thoughts for emerging and future directions.
Copyright © 2019 The Authors. Published by Elsevier B.V. All rights reserved.

Entities:  

Keywords:  Intrinsically disordered proteins; Liquid-liquid phase separation; Single-molecule FRET; Single-molecule biophysics

Mesh:

Substances:

Year:  2019        PMID: 31054969      PMCID: PMC6661187          DOI: 10.1016/j.bbapap.2019.04.007

Source DB:  PubMed          Journal:  Biochim Biophys Acta Proteins Proteom        ISSN: 1570-9639            Impact factor:   3.036


  84 in total

1.  mRNA structure determines specificity of a polyQ-driven phase separation.

Authors:  Erin M Langdon; Yupeng Qiu; Amirhossein Ghanbari Niaki; Grace A McLaughlin; Chase A Weidmann; Therese M Gerbich; Jean A Smith; John M Crutchley; Christina M Termini; Kevin M Weeks; Sua Myong; Amy S Gladfelter
Journal:  Science       Date:  2018-04-12       Impact factor: 47.728

2.  Active liquid-like behavior of nucleoli determines their size and shape in Xenopus laevis oocytes.

Authors:  Clifford P Brangwynne; Timothy J Mitchison; Anthony A Hyman
Journal:  Proc Natl Acad Sci U S A       Date:  2011-02-28       Impact factor: 11.205

3.  The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics.

Authors:  Shana Elbaum-Garfinkle; Younghoon Kim; Krzysztof Szczepaniak; Carlos Chih-Hsiung Chen; Christian R Eckmann; Sua Myong; Clifford P Brangwynne
Journal:  Proc Natl Acad Sci U S A       Date:  2015-05-26       Impact factor: 11.205

4.  Three-Color Single-Molecule FRET and Fluorescence Lifetime Analysis of Fast Protein Folding.

Authors:  Janghyun Yoo; John M Louis; Irina V Gopich; Hoi Sung Chung
Journal:  J Phys Chem B       Date:  2018-10-10       Impact factor: 2.991

5.  Structural polymorphism in the N-terminal oligomerization domain of NPM1.

Authors:  Diana M Mitrea; Christy R Grace; Marija Buljan; Mi-Kyung Yun; Nicholas J Pytel; John Satumba; Amanda Nourse; Cheon-Gil Park; M Madan Babu; Stephen W White; Richard W Kriwacki
Journal:  Proc Natl Acad Sci U S A       Date:  2014-03-10       Impact factor: 11.205

6.  Site-Specific Three-Color Labeling of α-Synuclein via Conjugation to Uniquely Reactive Cysteines during Assembly by Native Chemical Ligation.

Authors:  Taehyung C Lee; Crystal R Moran; Philip A Cistrone; Philip E Dawson; Ashok A Deniz
Journal:  Cell Chem Biol       Date:  2018-04-19       Impact factor: 8.116

7.  Using a FRET Library with Multiple Probe Pairs To Drive Monte Carlo Simulations of α-Synuclein.

Authors:  John J Ferrie; Conor M Haney; Jimin Yoon; Buyan Pan; Yi-Chih Lin; Zahra Fakhraai; Elizabeth Rhoades; Abhinav Nath; E James Petersson
Journal:  Biophys J       Date:  2018-01-09       Impact factor: 4.033

8.  Fluorescence correlation spectroscopy shows that monomeric polyglutamine molecules form collapsed structures in aqueous solutions.

Authors:  Scott L Crick; Murali Jayaraman; Carl Frieden; Ronald Wetzel; Rohit V Pappu
Journal:  Proc Natl Acad Sci U S A       Date:  2006-10-30       Impact factor: 11.205

9.  The conformational ensembles of α-synuclein and tau: combining single-molecule FRET and simulations.

Authors:  Abhinav Nath; Maria Sammalkorpi; David C DeWitt; Adam J Trexler; Shana Elbaum-Garfinkle; Corey S O'Hern; Elizabeth Rhoades
Journal:  Biophys J       Date:  2012-11-07       Impact factor: 4.033

10.  Modulating the intrinsic disorder in the cytoplasmic domain alters the biological activity of the N-methyl-D-aspartate-sensitive glutamate receptor.

Authors:  Ucheor B Choi; Rashek Kazi; Natalie Stenzoski; Lonnie P Wollmuth; Vladimir N Uversky; Mark E Bowen
Journal:  J Biol Chem       Date:  2013-06-19       Impact factor: 5.157

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  9 in total

Review 1.  Conformational Dynamics of Intrinsically Disordered Proteins Regulate Biomolecular Condensate Chemistry.

Authors:  Anton Abyzov; Martin Blackledge; Markus Zweckstetter
Journal:  Chem Rev       Date:  2022-02-18       Impact factor: 60.622

Review 2.  Conformational Freedom and Topological Confinement of Proteins in Biomolecular Condensates.

Authors:  Daniel Scholl; Ashok A Deniz
Journal:  J Mol Biol       Date:  2021-11-09       Impact factor: 5.469

Review 3.  Molecular structure in biomolecular condensates.

Authors:  Ivan Peran; Tanja Mittag
Journal:  Curr Opin Struct Biol       Date:  2019-11-29       Impact factor: 6.809

Review 4.  FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices.

Authors:  Eitan Lerner; Anders Barth; Jelle Hendrix; Benjamin Ambrose; Victoria Birkedal; Scott C Blanchard; Richard Börner; Hoi Sung Chung; Thorben Cordes; Timothy D Craggs; Ashok A Deniz; Jiajie Diao; Jingyi Fei; Ruben L Gonzalez; Irina V Gopich; Taekjip Ha; Christian A Hanke; Gilad Haran; Nikos S Hatzakis; Sungchul Hohng; Seok-Cheol Hong; Thorsten Hugel; Antonino Ingargiola; Chirlmin Joo; Achillefs N Kapanidis; Harold D Kim; Ted Laurence; Nam Ki Lee; Tae-Hee Lee; Edward A Lemke; Emmanuel Margeat; Jens Michaelis; Xavier Michalet; Sua Myong; Daniel Nettels; Thomas-Otavio Peulen; Evelyn Ploetz; Yair Razvag; Nicole C Robb; Benjamin Schuler; Hamid Soleimaninejad; Chun Tang; Reza Vafabakhsh; Don C Lamb; Claus Am Seidel; Shimon Weiss
Journal:  Elife       Date:  2021-03-29       Impact factor: 8.140

5.  Integrative structural dynamics probing of the conformational heterogeneity in synaptosomal-associated protein 25.

Authors:  Nabanita Saikia; Inna S Yanez-Orozco; Ruoyi Qiu; Pengyu Hao; Sergey Milikisiyants; Erkang Ou; George L Hamilton; Keith R Weninger; Tatyana I Smirnova; Hugo Sanabria; Feng Ding
Journal:  Cell Rep Phys Sci       Date:  2021-10-15

6.  Quantitative Description of Intrinsically Disordered Proteins Using Single-Molecule FRET, NMR, and SAXS.

Authors:  Samuel Naudi-Fabra; Maud Tengo; Malene Ringkjøbing Jensen; Martin Blackledge; Sigrid Milles
Journal:  J Am Chem Soc       Date:  2021-11-24       Impact factor: 15.419

Review 7.  Common Functions of Disordered Proteins across Evolutionary Distant Organisms.

Authors:  Arndt Wallmann; Christopher Kesten
Journal:  Int J Mol Sci       Date:  2020-03-19       Impact factor: 5.923

Review 8.  New technologies to analyse protein function: an intrinsic disorder perspective.

Authors:  Vladimir N Uversky
Journal:  F1000Res       Date:  2020-02-10

9.  Ratiometric Single-Molecule FRET Measurements to Probe Conformational Subpopulations of Intrinsically Disordered Proteins.

Authors:  Irem Nasir; Emily P Bentley; Ashok A Deniz
Journal:  Curr Protoc Chem Biol       Date:  2020-03
  9 in total

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