Phase-Separated Biomolecular Condensates

ISBN-13: 9781071626658 / Angielski / Miękka / 2022

Opis

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. 

Spis treści

Preface…

Table of Contents…

Contributing Authors…

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

Konstantinos Mazarakos, Sanbo Qin, and Huan-Xiang Zhou

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

Saeed Najafi, James McCarty, Kris T. Delaney, Glenn H. Fredrickson, and Joan-Emma Shea

3. 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, and Hue Sun Chan

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

Garrett M. Ginell and Alex S. Holehouse

5. Multi-Scale Modeling of Protein-RNA Condensation In and Out of Equilibrium

Rabia Laghmach, Isha Malhotra, and Davit A. Potoyan

6. Fluorescence Lifetime Imaging Microscopy of Biomolecular Condensates

My Diem Quan. Shih-Chu Leff Liao, Josephine C. Ferreon, and Allan Chris M. Ferreon

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

Laura R. Ganser, Yingda Ge, and Sua Myong

8. Fluorescence Correlation Spectroscopy and Phase Separation

Juan Jeremías Incicco, Debjit Roy, Melissa D. Stuchell-Brereton, and Andrea Soranno

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

Ibraheem Alshareedah and Priya R. Banerjee

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

Linyu Zuo, Luhua Lai, and Zhi Qi

11. Phase Separation-Based Biochemical Assays for Biomolecular Interactions

Gaofeng Pei, Min Zhou, Weifan Xu, Jing Wang, and Pilong Li

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

Archishman Ghosh, Divya Kota, and Huan-Xiang Zhou

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

Yichen Li, Jinge Gu, Cong Liu, and Dan Li

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

Huping Wang and Manajit Hayer-Hartl

15. Cryo-Electron Tomography of Reconstituted Biomolecular Condensate

Fergus Tollervey, Xiaojie Zhang, Mainak Bose, Jenny Sachweh, Jeffrey B. Woodruff, Titus M. Franzmann, and Julia Mahamid

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

Lara A. Gruijs da Silva and Dorothee Dormann

17. Synthetic Organelles for Multiple mRNA Selective Genetic Code Expansion in Eukaryotes

Christopher D. Reinkemeier and Edward A. Lemke

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

Baljyot Singh Parmar and Stephanie C. Weber

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

Chaelim Kim and Yongdae Shin

20. Assessing the Phase Separation Propensity of Proteins in Living Cells Through Optodroplet Formation 

Anne Rademacher, Fabian Erdel, Robin Weinmann, and Karsten Rippe

21. Mass Balance Imaging: A Phase Portrait Analysis for Characterizing Growth Kinetics of Biomolecular Condensates 

Jan Giesler, Victoria Tianjing Yan, Stephan Grill, and Arjun Narayanan

22. Characterizing Properties of Biomolecular Condensates Below the Diffraction Limit In Vivo

Ganesh Pandey, Alisha Budhathoki, and Jan-Hendrik Spille

Subject Index List…