Literature DB >> 33453924

Methods for characterizing the material properties of biomolecular condensates.

Ibraheem Alshareedah1, Taranpreet Kaur1, Priya R Banerjee2.   

Abstract

Biomolecular condensates are membrane-less sub-cellular compartments that perform a plethora of important functions in signaling and storage. The material properties of biomolecular condensates such as viscosity, surface tension, viscoelasticity, and macromolecular diffusion play important roles in regulating their biological functions. Aberrations in these properties have been implicated in various neurodegenerative disorders and certain types of cancer. Unraveling the molecular driving forces that control the fluid structure and dynamics of biomolecular condensates across different length- and time-scales necessitates the application of innovative biophysical methodologies. In this chapter, we discuss major experimental techniques that are widely used to study the material states and dynamics of biomolecular condensates as well as their practical and conceptual limitations. We end this chapter with a discussion on more advanced tools that are currently emerging to address the complex fluid dynamics of these condensates.
© 2021 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Condensate viscoelasticity; FRAP; Fluorescence microscopy; Liquid-liquid phase separation; Microrheology; Optical tweezers; Particle tracking

Mesh:

Substances:

Year:  2020        PMID: 33453924      PMCID: PMC7849318          DOI: 10.1016/bs.mie.2020.06.009

Source DB:  PubMed          Journal:  Methods Enzymol        ISSN: 0076-6879            Impact factor:   1.600


  57 in total

1.  A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation.

Authors:  Avinash Patel; Hyun O Lee; Louise Jawerth; Shovamayee Maharana; Marcus Jahnel; Marco Y Hein; Stoyno Stoynov; Julia Mahamid; Shambaditya Saha; Titus M Franzmann; Andrej Pozniakovski; Ina Poser; Nicola Maghelli; Loic A Royer; Martin Weigert; Eugene W Myers; Stephan Grill; David Drechsel; Anthony A Hyman; Simon Alberti
Journal:  Cell       Date:  2015-08-27       Impact factor: 41.582

2.  Measuring the complete force field of an optical trap.

Authors:  Marcus Jahnel; Martin Behrndt; Anita Jannasch; Erik Schäffer; Stephan W Grill
Journal:  Opt Lett       Date:  2011-04-01       Impact factor: 3.776

3.  Mobility measurement by analysis of fluorescence photobleaching recovery kinetics.

Authors:  D Axelrod; D E Koppel; J Schlessinger; E Elson; W W Webb
Journal:  Biophys J       Date:  1976-09       Impact factor: 4.033

4.  Theoretical analysis of fluorescence photobleaching recovery experiments.

Authors:  D M Soumpasis
Journal:  Biophys J       Date:  1983-01       Impact factor: 4.033

5.  Interplay between Short-Range Attraction and Long-Range Repulsion Controls Reentrant Liquid Condensation of Ribonucleoprotein-RNA Complexes.

Authors:  Ibraheem Alshareedah; Taranpreet Kaur; Jason Ngo; Hannah Seppala; Liz-Audrey Djomnang Kounatse; Wei Wang; Mahdi Muhammad Moosa; Priya R Banerjee
Journal:  J Am Chem Soc       Date:  2019-09-05       Impact factor: 15.419

6.  A new FRAP/FRAPa method for three-dimensional diffusion measurements based on multiphoton excitation microscopy.

Authors:  Davide Mazza; Kevin Braeckmans; Francesca Cella; Ilaria Testa; Dries Vercauteren; Jo Demeester; Stefaan S De Smedt; Alberto Diaspro
Journal:  Biophys J       Date:  2008-07-11       Impact factor: 4.033

7.  Simplified equation to extract diffusion coefficients from confocal FRAP data.

Authors:  Minchul Kang; Charles A Day; Anne K Kenworthy; Emmanuele DiBenedetto
Journal:  Traffic       Date:  2012-10-10       Impact factor: 6.215

8.  Phase transitions in the assembly of multivalent signalling proteins.

Authors:  Pilong Li; Sudeep Banjade; Hui-Chun Cheng; Soyeon Kim; Baoyu Chen; Liang Guo; Marc Llaguno; Javoris V Hollingsworth; David S King; Salman F Banani; Paul S Russo; Qiu-Xing Jiang; B Tracy Nixon; Michael K Rosen
Journal:  Nature       Date:  2012-03-07       Impact factor: 49.962

9.  ImageJ2: ImageJ for the next generation of scientific image data.

Authors:  Curtis T Rueden; Johannes Schindelin; Mark C Hiner; Barry E DeZonia; Alison E Walter; Ellen T Arena; Kevin W Eliceiri
Journal:  BMC Bioinformatics       Date:  2017-11-29       Impact factor: 3.169

10.  RNA-Induced Conformational Switching and Clustering of G3BP Drive Stress Granule Assembly by Condensation.

Authors:  Jordina Guillén-Boixet; Andrii Kopach; Alex S Holehouse; Sina Wittmann; Marcus Jahnel; Raimund Schlüßler; Kyoohyun Kim; Irmela R E A Trussina; Jie Wang; Daniel Mateju; Ina Poser; Shovamayee Maharana; Martine Ruer-Gruß; Doris Richter; Xiaojie Zhang; Young-Tae Chang; Jochen Guck; Alf Honigmann; Julia Mahamid; Anthony A Hyman; Rohit V Pappu; Simon Alberti; Titus M Franzmann
Journal:  Cell       Date:  2020-04-16       Impact factor: 41.582

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  5 in total

Review 1.  A conceptual framework for understanding phase separation and addressing open questions and challenges.

Authors:  Tanja Mittag; Rohit V Pappu
Journal:  Mol Cell       Date:  2022-06-07       Impact factor: 19.328

2.  Quantifying viscosity and surface tension of multicomponent protein-nucleic acid condensates.

Authors:  Ibraheem Alshareedah; George M Thurston; Priya R Banerjee
Journal:  Biophys J       Date:  2021-01-14       Impact factor: 4.033

3.  Compartmentalization of telomeres through DNA-scaffolded phase separation.

Authors:  Amanda Jack; Yoonji Kim; Amy R Strom; Daniel S W Lee; Byron Williams; Jeffrey M Schaub; Elizabeth H Kellogg; Ilya J Finkelstein; Luke S Ferro; Ahmet Yildiz; Clifford P Brangwynne
Journal:  Dev Cell       Date:  2022-01-24       Impact factor: 12.270

Review 4.  Rheology and Viscoelasticity of Proteins and Nucleic Acids Condensates.

Authors:  Davide Michieletto; Mattia Marenda
Journal:  JACS Au       Date:  2022-06-13

5.  Multi-channel AgNWs-doped interdigitated organic electrochemical transistors enable sputum-based device towards noninvasive and portable diagnosis of lung cancer.

Authors:  Ru Zhang; Jing Zhang; Fei Tan; Deqi Yang; Bingfang Wang; Jing Dai; Yin Qi; Linyu Ran; Wenjuan He; Yingying Lv; Feilong Wang; Yin Fang
Journal:  Mater Today Bio       Date:  2022-08-05
  5 in total

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