Literature DB >> 34144468

Biophysical studies of phase separation integrating experimental and computational methods.

Nicolas L Fawzi1, Sapun H Parekh2, Jeetain Mittal3.   

Abstract

Biomolecular phase separation that contributes to the formation of membraneless organelles and biomolecular condensates has recently gained tremendous attention because of the importance of these assemblies in physiology, disease, and engineering applications. Understanding and directing biomolecular phase separation requires a multiscale view of the biophysical properties of these phases. Yet, many classic tools to characterize biomolecular properties do not apply in these condensed phases. Here, we discuss insights obtained from spectroscopic methods, in particular nuclear magnetic resonance and optical spectroscopy, in understanding the molecular and atomic interactions that underlie the formation of protein-rich condensates. We also review approaches closely coupling nuclear magnetic resonance data with computational methods especially coarse-grained and all-atom molecular simulations, which provide insight into molecular features of phase separation. Finally, we point to future methodolical developments, particularly visualizing biophysical properties of condensates in cells.
Copyright © 2021 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  Advanced sampling techniques; Biomolecular condensates; Fluorescence lifetime imaging; Förster resonance energy transfer (FRET); Hyperspectral imaging; Magic angle spinning solid state NMR spectroscopy; Membraneless organelles; Molecular dynamics simulations; Phase separation; Protein nuclear magnetic resonance spectroscopy (NMR); Raman spectroscopy

Mesh:

Substances:

Year:  2021        PMID: 34144468      PMCID: PMC8530909          DOI: 10.1016/j.sbi.2021.04.004

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   7.786


  60 in total

1.  Phospho-dependent phase separation of FMRP and CAPRIN1 recapitulates regulation of translation and deadenylation.

Authors:  Tae Hun Kim; Brian Tsang; Robert M Vernon; Nahum Sonenberg; Lewis E Kay; Julie D Forman-Kay
Journal:  Science       Date:  2019-08-23       Impact factor: 47.728

2.  Alteration of Microstructure in Biopolymeric Hydrogels via Compositional Modification of Resilin-Like Polypeptides.

Authors:  Cristobal Garcia Garcia; Sai S Patkar; Nina Jovic; Jeetain Mittal; Kristi L Kiick
Journal:  ACS Biomater Sci Eng       Date:  2021-01-19

3.  Structure of FUS Protein Fibrils and Its Relevance to Self-Assembly and Phase Separation of Low-Complexity Domains.

Authors:  Dylan T Murray; Masato Kato; Yi Lin; Kent R Thurber; Ivan Hung; Steven L McKnight; Robert Tycko
Journal:  Cell       Date:  2017-09-21       Impact factor: 41.582

Review 4.  The (un)structural biology of biomolecular liquid-liquid phase separation using NMR spectroscopy.

Authors:  Anastasia C Murthy; Nicolas L Fawzi
Journal:  J Biol Chem       Date:  2020-01-07       Impact factor: 5.157

5.  A Molecular Grammar Governing the Driving Forces for Phase Separation of Prion-like RNA Binding Proteins.

Authors:  Jie Wang; Jeong-Mo Choi; Alex S Holehouse; Hyun O Lee; Xiaojie Zhang; Marcus Jahnel; Shovamayee Maharana; Régis Lemaitre; Andrei Pozniakovsky; David Drechsel; Ina Poser; Rohit V Pappu; Simon Alberti; Anthony A Hyman
Journal:  Cell       Date:  2018-06-28       Impact factor: 41.582

6.  The liquid structure of elastin.

Authors:  Sarah Rauscher; Régis Pomès
Journal:  Elife       Date:  2017-11-09       Impact factor: 8.140

7.  Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins.

Authors:  Tyler S Harmon; Alex S Holehouse; Michael K Rosen; Rohit V Pappu
Journal:  Elife       Date:  2017-11-01       Impact factor: 8.140

8.  NPM1 exhibits structural and dynamic heterogeneity upon phase separation with the p14ARF tumor suppressor.

Authors:  Eric Gibbs; Barbara Perrone; Alia Hassan; Rainer Kümmerle; Richard Kriwacki
Journal:  J Magn Reson       Date:  2019-11-11       Impact factor: 2.734

9.  The effects of cosolutes and crowding on the kinetics of protein condensate formation based on liquid-liquid phase separation: a pressure-jump relaxation study.

Authors:  Hasan Cinar; Roland Winter
Journal:  Sci Rep       Date:  2020-10-14       Impact factor: 4.379

10.  Biomolecular condensates amplify mRNA decapping by biasing enzyme conformation.

Authors:  Ryan W Tibble; Anaïs Depaix; Joanna Kowalska; Jacek Jemielity; John D Gross
Journal:  Nat Chem Biol       Date:  2021-03-25       Impact factor: 15.040

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  4 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.  Regulation of spatially restricted gene expression: linking RNA localization and phase separation.

Authors:  Liam C O'Connell; Kimberly L Mowry
Journal:  Biochem Soc Trans       Date:  2021-12-17       Impact factor: 5.407

3.  Atomic resolution dynamics of cohesive interactions in phase-separated Nup98 FG domains.

Authors:  Eszter E Najbauer; Sheung Chun Ng; Christian Griesinger; Dirk Görlich; Loren B Andreas
Journal:  Nat Commun       Date:  2022-03-21       Impact factor: 17.694

Review 4.  NMR Provides Unique Insight into the Functional Dynamics and Interactions of Intrinsically Disordered Proteins.

Authors:  Aldo R Camacho-Zarco; Vincent Schnapka; Serafima Guseva; Anton Abyzov; Wiktor Adamski; Sigrid Milles; Malene Ringkjøbing Jensen; Lukas Zidek; Nicola Salvi; Martin Blackledge
Journal:  Chem Rev       Date:  2022-04-21       Impact factor: 72.087

  4 in total

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