Biomolecular Interactions Part B

1st Edition, Volume 169 - May 12, 2022
Editor: Arun K. Shukla
Language: English
Hardback ISBN:
9 7 8 - 0 - 1 2 - 8 2 3 3 5 3 - 5
eBook ISBN:
9 7 8 - 0 - 1 2 - 8 2 3 3 5 4 - 2

Biomolecular Interactions: Part A, Volume 169, the latest release in the Methods in Cell Biology series, highlights new advances in the field, with this new volume presenting in… Read more

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Biomolecular Interactions: Part A, Volume 169, the latest release in the Methods in Cell Biology series, highlights new advances in the field, with this new volume presenting interesting chapters on a variety of timely topics, including Emerging Mechanisms of Targeted Protein Degradation by Molecular Glues, Design and use of programmable DNA Hydrogels, Oligomerization of membrane receptors: Approaches to measure in live cells, Interactions of alpha-synuclein with biomolecules, Gel-electrophoresis based method for biomolecular interaction, Recombinant centrosome expression in bacterial system, Reconstituting CCL5-CCR5 complex for structural and mechanistic analysis, Protein engineering and design in ion channel receptors, and much more.

Cover image
Title page
Table of Contents
Copyright
Contributors
Preface
Chapter 1: Emerging mechanisms of targeted protein degradation by molecular glues
Abstract
1: Introduction
2: Immunomodulatory imide drugs (IMiDs)
3: Splicing inhibitor sulfonamides (SPLAMs)
4: CDK12/13:DDB1 glues trigger cyclin K degradation
5: BCL6 glues induce polymerization and degradation of BCL6
6: Methods for measuring protein degradation
7: Bridging the gap from “serendegrity” to systematic screening
8: Protein degrader discovery by comparative drug profiling in hyponeddylated cell lines
9: Leveraging cell fate control elements for positive selection of protein degraders
10: Conclusions
References
Chapter 2: Visualizing G protein-coupled receptor homomers using photoactivatable dye localization microscopy
Abstract
1: Introduction
2: Materials
3: A step-by-step guide to PD-PALM imaging and analysis
4: Future directions
Acknowledgments
References
Chapter 3: Interaction of alpha-synuclein with lipids
Abstract
1: Introduction
2: Interaction of α-syn with lipid membranes
3: Factors modulating α-syn membrane binding
4: α-syn interaction with specific membranes and membrane regions
5: Membrane remodeling by α-syn
6: Conclusion
References
Chapter 4: Gel-electrophoresis based method for biomolecular interaction
Abstract
1: Introduction
2: Difference between SDS-PAGE, BN-PAGE and native gel electrophoresis
3: Materials
4: Methods
5: Examples
6: Concluding remarks
7: Notes
References
Chapter 5: Yeast 2-hybrid assay for investigating the interaction between the centrosome proteins PLK4 and STIL
Abstract
1: Introduction
2: Material
3: Protocol
4: Results
5: Discussion
6: Troubleshooting
References
Chapter 6: Preparation of a stable CCL5·CCR5·Gi signaling complex for Cryo-EM analysis
Abstract
1: Introduction
2: Methods
3: Discussion and conclusion
References
Chapter 7: Protein engineering and design in ion channels and receptors
Abstract
1: Introduction
2: Materials
3: Methods
4: Receptor engineering and design
5: Concluding remarks
References
Chapter 8: Discovery of Virus-Host interactions using bioinformatic tools
Abstract
1: Introduction to Virus-Host interactions
2: Virus-Host databases
3: Omics data
4: Artificial intelligence approaches
5: Virus-Host interaction network approaches
6: Virus-Host interaction structural prediction
7: Conclusions
References
Chapter 9: Best practices for resilient automation of biomolecular simulations
Abstract
1: Introduction
2: Common problems and approaches to solving them
3: Conclusion
4: Script to generate next equilibrium MD simulation: “next_namd_prod.py”
5: Script to facilitate automated resilient FEP calculations using NAMD
6: Sample analysis script
References
Chapter 10: Label-free impedance measurements to unravel biomolecular interactions involved in G protein-coupled receptor signaling
Abstract
1: Introduction
2: Electrochemical impedance measurements to study ligand-receptor interactions
3: Agonist and antagonist assays
4: Dose-response studies
5: In-depth analysis of the signal transduction pathway
6: Receptor desensitization
7: Further experimental options and current developments
Acknowledgments
References
Chapter 11: Proximity labeling for investigating protein-protein interactions
Abstract
1: Introduction
2: Nonproximity labeling based methods for studying protein-protein interactions
3: Proximity labeling methods for studying protein-protein interactions
4: Coupling mass spectrometry to proximity labeling
5: Advantages and disadvantages of the different methods
6: Summary
References
Chapter 12: An intrabody sensor to monitor conformational activation of β-arrestins
Abstract
1: Introduction
2: Materials
3: Methods
4: Concluding remarks
Acknowledgment
References
Chapter 13: Nanoluciferase-based methods to monitor activation, modulation and trafficking of atypical chemokine receptors
Abstract
1: Introduction
2: Materials
3: Methods
4: Controls and additional considerations
5: Concluding remarks
6: Notes
Acknowledgments
References
Chapter 14: In-cellulo chemical cross-linking to visualize protein-protein interactions
Abstract
1: Introduction
2: Materials and methods
3: Troubleshooting
4: Additional considerations
5: Concluding remarks
Acknowledgment
References
Chapter 15: Nanoluciferase-based complementation assay for systematic profiling of GPCR–GRK interactions
Abstract
1: Introduction
2: Materials
3: Methods
4: Notes
Acknowledgments
References
Chapter 16: DNA hydrogels: Principles, synthesis, characterization and applications to cell biology
Abstract
1: Introduction
2: Principle
3: Synthesis methods
4: Characterization
5: Applications
6: Conclusions and future directions
Acknowledgments
References

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Arun K. Shukla