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Phase-Separated Biomolecular Condensates

Methods and Protocols

  • Book
  • © 2023

Overview

Editors:
  1. Huan-Xiang Zhou

    1. Department of Chemistry, University of Illinois at Chicago, Chicago, USA

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    You can also search for this editor in PubMed   Google Scholar

  2. Jan-Hendrik Spille

    1. Department of Physics, University of Illinois at Chicago, Chicago, USA

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    You can also search for this editor in PubMed   Google Scholar

  3. Priya R. Banerjee

    1. Department of Physics, University at Buffalo, State University, Buffalo, USA

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    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2563)

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Table of contents (22 protocols)

  1. Front Matter

    Pages i-xiv
    Download chapter PDF

  2. Calculating Binodals and Interfacial Tension of Phase-Separated Condensates from Molecular Simulations with Finite-Size Corrections

    • Konstantinos Mazarakos, Sanbo Qin, Huan-Xiang Zhou
    Pages 1-35

  3. Field-Theoretic Simulation Method to Study the Liquid–Liquid Phase Separation of Polymers

    • Saeed Najafi, James McCarty, Kris T. Delaney, Glenn H. Fredrickson, Joan-Emma Shea
    Pages 37-49

  4. Numerical Techniques for Applications of Analytical Theories to Sequence-Dependent Phase Separations of Intrinsically Disordered Proteins

    • Yi-Hsuan Lin, Jonas Wessén, Tanmoy Pal, Suman Das, Hue Sun Chan
    Pages 51-94

  5. An Introduction to the Stickers-and-Spacers Framework as Applied to Biomolecular Condensates

    • Garrett M. Ginell, Alex S. Holehouse
    Pages 95-116

  6. Multiscale Modeling of Protein-RNA Condensation in and Out of Equilibrium

    • Rabia Laghmach, Isha Malhotra, Davit A. Potoyan
    Pages 117-133

  7. Fluorescence Lifetime Imaging Microscopy of Biomolecular Condensates

    • My Diem Quan, Shih-Chu Jeff Liao, Josephine C. Ferreon, Allan Chris M. Ferreon
    Pages 135-148

  8. Single-Molecule Fluorescence Methods to Study Protein-RNA Interactions Underlying Biomolecular Condensates

    • Laura R. Ganser, Yingda Ge, Sua Myong
    Pages 149-160

  9. Fluorescence Correlation Spectroscopy and Phase Separation

    • Juan Jeremías Incicco, Debjit Roy, Melissa D. Stuchell-Brereton, Andrea Soranno
    Pages 161-198

  10. Measurement of Protein and Nucleic Acid Diffusion Coefficients Within Biomolecular Condensates Using In-Droplet Fluorescence Correlation Spectroscopy

    • Ibraheem Alshareedah, Priya R. Banerjee
    Pages 199-213

  11. Single-Molecule Imaging of the Phase Separation-Modulated DNA Compaction to Study Transcriptional Repression

    • Linyu Zuo, Luhua Lai, Zhi Qi
    Pages 215-223

  12. Phase Separation-Based Biochemical Assays for Biomolecular Interactions

    • Gaofeng Pei, Min Zhou, Weifan Xu, Jing Wang, Pilong Li
    Pages 225-236

  13. Determining Thermodynamic and Material Properties of Biomolecular Condensates by Confocal Microscopy and Optical Tweezers

    • Archishman Ghosh, Divya Kota, Huan-Xiang Zhou
    Pages 237-260

  14. A High-Throughput Method to Profile Protein Liquid-Liquid Phase Separation

    • Yichen Li, Jinge Gu, Cong Liu, Dan Li
    Pages 261-268

  15. Phase Separation of Rubisco by the Folded SSUL Domains of CcmM in Beta-Carboxysome Biogenesis

    • Huping Wang, Manajit Hayer-Hartl
    Pages 269-296

  16. Cryo-Electron Tomography of Reconstituted Biomolecular Condensates

    • Fergus Tollervey, Xiaojie Zhang, Mainak Bose, Jenny Sachweh, Jeffrey B. Woodruff, Titus M. Franzmann et al.
    Pages 297-324

  17. Sedimentation Assays to Assess the Impact of Posttranslational Modifications on Phase Separation of RNA-Binding Proteins In Vitro and In Cells

    • Lara A. Gruijs da Silva, Dorothee Dormann
    Pages 325-339

  18. Synthetic Organelles for Multiple mRNA Selective Genetic Code Expansions in Eukaryotes

    • Christopher D. Reinkemeier, Edward A. Lemke
    Pages 341-369

  19. Single-Molecule Tracking of RNA Polymerase In and Out of Condensates in Live Bacterial Cells

    • Baljyot Singh Parmar, Stephanie C. Weber
    Pages 371-381

  20. An Optogenetic Toolkit for the Control of Phase Separation in Living Cells

    • Chaelim Kim, Yongdae Shin
    Pages 383-394
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Keywords

About this book

This volume provides readers with a broad collection of theoretical, computational, and experimental methods to quantitatively study the properties of phase-separate biomolecular condensates in diverse systems. The chapters in this book cover topics such as theoretical and computational methods; methods for in vitro characterization of biomolecular condensates; and techniques that enable in-cell characterization of biomolecular condensates. Written in the highly successful Methods in Molecular Biology series format, chapters include introduction to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and expert tips on troubleshooting and avoiding known pitfalls.

Comprehensive and thorough, Phase-Separated Biomolecular Condensates: Methods and Protocols is a valuable resource that helps researchers learn and use established methods to study both biophysical properties and biological functions of biomolecular condensates. 



Editors and Affiliations

  • Department of Chemistry, University of Illinois at Chicago, Chicago, USA

    Huan-Xiang Zhou

  • Department of Physics, University of Illinois at Chicago, Chicago, USA

    Jan-Hendrik Spille

  • Department of Physics, University at Buffalo, State University, Buffalo, USA

    Priya R. Banerjee

Bibliographic Information

  • Book Title: Phase-Separated Biomolecular Condensates

  • Book Subtitle: Methods and Protocols

  • Editors: Huan-Xiang Zhou, Jan-Hendrik Spille, Priya R. Banerjee

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-2663-4

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2023

  • Hardcover ISBN: 978-1-0716-2662-7Published: 14 October 2022

  • Softcover ISBN: 978-1-0716-2665-8Published: 14 October 2022

  • eBook ISBN: 978-1-0716-2663-4Published: 13 October 2022

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIV, 449

  • Number of Illustrations: 1 b/w illustrations

  • Topics: Biochemistry, general, Bioinformatics

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