Literature DB >> 33469149

A generic approach to study the kinetics of liquid-liquid phase separation under near-native conditions.

Joris Van Lindt1,2, Anna Bratek-Skicki3,4, Phuong N Nguyen1,2,5, Donya Pakravan6,7, Luis F Durán-Armenta1,2, Agnes Tantos8, Rita Pancsa8, Ludo Van Den Bosch6,7, Dominique Maes2, Peter Tompa9,10,11.   

Abstract

Understanding the kinetics, thermodynamics, and molecular mechanisms of liquid-liquid phase separation (LLPS) is of paramount importance in cell biology, requiring reproducible methods for studying often severely aggregation-prone proteins. Frequently applied approaches for inducing LLPS, such as dilution of the protein from an urea-containing solution or cleavage of its fused solubility tag, often lead to very different kinetic behaviors. Here we demonstrate that at carefully selected pH values proteins such as the low-complexity domain of hnRNPA2, TDP-43, and NUP98, or the stress protein ERD14, can be kept in solution and their LLPS can then be induced by a jump to native pH. This approach represents a generic method for studying the full kinetic trajectory of LLPS under near native conditions that can be easily controlled, providing a platform for the characterization of physiologically relevant phase-separation behavior of diverse proteins.

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Year:  2021        PMID: 33469149      PMCID: PMC7815728          DOI: 10.1038/s42003-020-01596-8

Source DB:  PubMed          Journal:  Commun Biol        ISSN: 2399-3642


  23 in total

1.  Amyloid fibril formation by an SH3 domain.

Authors:  J I Guijarro; M Sunde; J A Jones; I D Campbell; C M Dobson
Journal:  Proc Natl Acad Sci U S A       Date:  1998-04-14       Impact factor: 11.205

2.  The role of liquid-liquid phase separation in aggregation of the TDP-43 low-complexity domain.

Authors:  W Michael Babinchak; Raza Haider; Benjamin K Dumm; Prottusha Sarkar; Krystyna Surewicz; Jin-Kyu Choi; Witold K Surewicz
Journal:  J Biol Chem       Date:  2019-02-27       Impact factor: 5.157

3.  Physical principles of intracellular organization via active and passive phase transitions.

Authors:  Joel Berry; Clifford P Brangwynne; Mikko Haataja
Journal:  Rep Prog Phys       Date:  2018-01-09

4.  Salt Interactions in Solution Prevent Direct Association of Urea with a Peptide Backbone.

Authors:  Nicola Steinke; Anna Genina; Christian D Lorenz; Sylvia E McLain
Journal:  J Phys Chem B       Date:  2017-02-14       Impact factor: 2.991

5.  Mechanistic View of hnRNPA2 Low-Complexity Domain Structure, Interactions, and Phase Separation Altered by Mutation and Arginine Methylation.

Authors:  Veronica H Ryan; Gregory L Dignon; Gül H Zerze; Charlene V Chabata; Rute Silva; Alexander E Conicella; Joshua Amaya; Kathleen A Burke; Jeetain Mittal; Nicolas L Fawzi
Journal:  Mol Cell       Date:  2018-01-18       Impact factor: 17.970

6.  Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding.

Authors:  Lan Hua; Ruhong Zhou; D Thirumalai; B J Berne
Journal:  Proc Natl Acad Sci U S A       Date:  2008-10-28       Impact factor: 11.205

7.  Tuning phase transitions of aqueous protein solutions by multivalent cations.

Authors:  Olga Matsarskaia; Felix Roosen-Runge; Gudrun Lotze; Johannes Möller; Alessandro Mariani; Fajun Zhang; Frank Schreiber
Journal:  Phys Chem Chem Phys       Date:  2018-10-31       Impact factor: 3.676

8.  Residue-by-Residue View of In Vitro FUS Granules that Bind the C-Terminal Domain of RNA Polymerase II.

Authors:  Kathleen A Burke; Abigail M Janke; Christy L Rhine; Nicolas L Fawzi
Journal:  Mol Cell       Date:  2015-10-08       Impact factor: 17.970

9.  A pH-driven transition of the cytoplasm from a fluid- to a solid-like state promotes entry into dormancy.

Authors:  Matthias Christoph Munder; Daniel Midtvedt; Titus Franzmann; Elisabeth Nüske; Oliver Otto; Maik Herbig; Elke Ulbricht; Paul Müller; Anna Taubenberger; Shovamayee Maharana; Liliana Malinovska; Doris Richter; Jochen Guck; Vasily Zaburdaev; Simon Alberti
Journal:  Elife       Date:  2016-03-22       Impact factor: 8.140

Review 10.  Stress granules as crucibles of ALS pathogenesis.

Authors:  Yun R Li; Oliver D King; James Shorter; Aaron D Gitler
Journal:  J Cell Biol       Date:  2013-04-29       Impact factor: 10.539

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  10 in total

Review 1.  Liquid-liquid phase separation as an organizing principle of intracellular space: overview of the evolution of the cell compartmentalization concept.

Authors:  Iuliia A Antifeeva; Alexander V Fonin; Anna S Fefilova; Olesya V Stepanenko; Olga I Povarova; Sergey A Silonov; Irina M Kuznetsova; Vladimir N Uversky; Konstantin K Turoverov
Journal:  Cell Mol Life Sci       Date:  2022-04-20       Impact factor: 9.261

2.  Molecular interactions of FG nucleoporin repeats at high resolution.

Authors:  Alain Ibáñez de Opakua; James A Geraets; Benedikt Frieg; Christian Dienemann; Adriana Savastano; Marija Rankovic; Maria-Sol Cima-Omori; Gunnar F Schröder; Markus Zweckstetter
Journal:  Nat Chem       Date:  2022-09-22       Impact factor: 24.274

3.  Modulation of assembly of TDP-43 low-complexity domain by heparin: From droplets to amyloid fibrils.

Authors:  Dushyant Kumar Garg; Rajiv Bhat
Journal:  Biophys J       Date:  2022-05-28       Impact factor: 3.699

4.  Molecular crowding and RNA synergize to promote phase separation, microtubule interaction, and seeding of Tau condensates.

Authors:  Janine Hochmair; Christian Exner; Maximilian Franck; Alvaro Dominguez-Baquero; Lisa Diez; Hévila Brognaro; Matthew L Kraushar; Thorsten Mielke; Helena Radbruch; Senthilvelrajan Kaniyappan; Sven Falke; Eckhard Mandelkow; Christian Betzel; Susanne Wegmann
Journal:  EMBO J       Date:  2022-03-17       Impact factor: 14.012

5.  F/YGG-motif is an intrinsically disordered nucleic-acid binding motif.

Authors:  Joris Van Lindt; Tamas Lazar; Donya Pakravan; Manon Demulder; Attila Meszaros; Ludo Van Den Bosch; Dominique Maes; Peter Tompa
Journal:  RNA Biol       Date:  2021-12-31       Impact factor: 4.766

6.  DispHScan: A Multi-Sequence Web Tool for Predicting Protein Disorder as a Function of pH.

Authors:  Carlos Pintado-Grima; Valentín Iglesias; Jaime Santos; Vladimir N Uversky; Salvador Ventura
Journal:  Biomolecules       Date:  2021-10-28

7.  The HIV-1 Nucleocapsid Regulates Its Own Condensation by Phase-Separated Activity-Enhancing Sequestration of the Viral Protease during Maturation.

Authors:  Sébastien Lyonnais; S Kashif Sadiq; Cristina Lorca-Oró; Laure Dufau; Sara Nieto-Marquez; Tuixent Escribà; Natalia Gabrielli; Xiao Tan; Mohamed Ouizougun-Oubari; Josephine Okoronkwo; Michèle Reboud-Ravaux; José Maria Gatell; Roland Marquet; Jean-Christophe Paillart; Andreas Meyerhans; Carine Tisné; Robert J Gorelick; Gilles Mirambeau
Journal:  Viruses       Date:  2021-11-19       Impact factor: 5.048

Review 8.  Melatonin: Regulation of Prion Protein Phase Separation in Cancer Multidrug Resistance.

Authors:  Doris Loh; Russel J Reiter
Journal:  Molecules       Date:  2022-01-21       Impact factor: 4.411

9.  Temporal and spatial characterisation of protein liquid-liquid phase separation using NMR spectroscopy.

Authors:  Jack E Bramham; Alexander P Golovanov
Journal:  Nat Commun       Date:  2022-04-01       Impact factor: 17.694

10.  In-Silico Analysis of pH-Dependent Liquid-Liquid Phase Separation in Intrinsically Disordered Proteins.

Authors:  Carlos Pintado-Grima; Oriol Bárcenas; Salvador Ventura
Journal:  Biomolecules       Date:  2022-07-12
  10 in total

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