Protein-Protein Interactions

ISBN-13: 9781071633267 / Angielski / Twarda / 2023

Opis

This detailed volume provides a comprehensive collection of classic and cutting-edge methods and techniques in mapping protein-protein interactions. The chapters include a variety of in vitro and in vivo experimental methods covering cell biology, biochemistry, and biophysics. In addition, the book also explores in silico methods including sequence-, structure-, and phylogenetic profile-based approaches as well as gene expression and machine learning methods. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, as well as tips on troubleshooting and avoiding known pitfalls. 

Authoritative and practical, Protein-Protein Interactions: Methods and Protocols serves as an ideal guide for researchers working in protein science and beyond.

Spis treści

1. Yeast-Two-Hybrid Technique to Identify Protein-Protein Interactions

            Prabu Gnanasekaran and Hanu R. Pappu

 

2. Cytotrap: An Innovative Approach for Protein-Protein Interaction Studies for Cytoplasmic Proteins

            Binoop Mohan, Doni Devi Thingujam, and Karolina M. Pajerowska-Mukhtar

 

3. Analyzing Protein-Protein Interactions Using the Split-Ubiquitin System

            Rucha Karnik and Michael R. Blatt

 

4. Detection of Protein–Protein Interactions Utilizing the Split-Ubiquitin Membrane-Based Yeast Two-Hybrid System

            Siddhartha Dutta and Matthew D. Smith

 

5. Preparation and Utilization of a Versatile GFP-Protein Trap-Like System for Protein Complex Immunoprecipitation in Plants

            Danish Diwan and Karolina M. Pajerowska-Mukhtar

 

6. Tandem Affinity Purification (TAP) of Interacting Prey Proteins with FLAG- and HA-Tagged Bait Proteins

            Teck Yew Low and Pey Yee Lee

 

7. Affinity Purification-Mass Spectroscopy (AP-MS) and Co-Immunoprecipitation (Co-IP) Technique to Study Protein-Protein Interactions

            Prabu Gnanasekaran and Hanu R. Pappu

 

8. Co-Immunoprecipitation-Based Identification of Effector-Host Protein Interactions from Pathogen-Infected Plant Tissue

            Mamoona Khan and Armin Djamei

 

9. Co-Immunoprecipitation for Assessing Protein-Protein Interactions in Agrobacterium-Mediated Transient Expression System in Nicotiana benthamiana

            Ji Chul Nam, Padam S. Bhatt, Sung-Il Kim, and Hong-Gu Kang

 

10. Detection of Protein-Protein Interactions Using Glutathione-S-Transferase (GST) Pull-Down Assay Technique

            Prabu Gnanasekaran and Hanu R. Pappu

 

11. Bimolecular Fluorescence Complementation (BiFC) Assay to Visualize Protein-Protein Interactions in Living Cells

            Prabu Gnanasekaran and Hanu R. Pappu

 

12. Detecting Protein-Protein Interactions Using Bimolecular Fluorescence Complementation (BiFC) and Luciferase Complementation Assays (LCA)

            Pepijn Bais, Louai Alidrissi, and Ikram Blilou

 

13. Forster Resonance Energy Transfer (FRET) to Visualize Protein-Protein Interactions in the Plant Cell

            Prabu Gnanasekaran and Hanu R. Pappu

 

14. Dynamic Proximity Tagging in Living Plant Cells with Pupylation-Based Interaction Tagging

            Ruiqiang Ye, Zhuoran Lin, Kun-Hsaing Liu, Jen Sheen, and Sixue Chen

 

15. Characterization of Small Molecule-Protein Interactions Using SPR Method

            Binmei Sun, Jianmei Xu, Shaoqun Liu, and Qing X. Li

 

16. High-Throughput Protein-Protein Interactions Screening Using Pool-Based Liquid Yeast Two-Hybrid Pipeline

            Benoît Castandet, Claire Lurin, Étienne Delannoy, and Dario Monachello

 

17. Dynamic Enrichment for Evaluation of Protein Networks (DEEPN): A High Throughput Yeast Two-Hybrid (Y2H) Protocol to Evaluate Networks

            Ali Zeeshan Fakhar, Jinbao Liu, and Karolina M. Pajerowska-Mukhtar

 

18. An Interactome Assay for Detecting Interactions between Extracellular Domains of Receptor Kinases

            Jente Stouthamer, Sergio Martin-Ramirez, and Elwira Smakowska-Luzan

 

19. Next-Generation Yeast Two-Hybrid Screening to Discover Protein-Protein Interactions

            J. Mitch Elmore, Valeria Velásquez-Zapata, and Roger P. Wise

 

20. Bioinformatic Analysis of Yeast Two-Hybrid Next-Generation Interaction Screen Data

            Valeria Velásquez-Zapata, J. Mitch Elmore, and Roger P. Wise

 

21. Discovering Protein-Protein Interactions Using Co-Fractionation-Mass Spectrometry with Label-Free Quantitation

            Mopelola O. Akinlaja, R. Greg. Stacey, Queenie W. T. Chan, and Leonard J. Foster

 

22. Protein-Protein Interaction Network Mapping by Affinity Purification Cross-Linking (AP-CXL-MS) Proteomics

            Ashima Mehta, Abu Hena Mostafa Kamal, Sharel Cornelius, and Saiful M. Chowdhury

 

23. Protein Interaction Screen on a Peptide Matrix (PrISMa)

            Daniel Perez-Hernandez, Mattson Jones, and Gunnar Dittmar

 

24. Analyzing Protein Interactions by MAC-Tag Approaches

            Xiaonan Liu, Kari Salokas, Salla Keskitalo, Patricia Martínez-Botía, and Markku Varjosalo

 

25. Identification and Quantification of Affinity-Purified Proteins with MaxQuant, Followed by the Discrimination of Nonspecific Interactions with the CRAPome Interface

            Pey Yee Lee and Teck Yew Low

 

26. Cataloguing Protein Complexes In Planta Using TurboID-Catalyzed Proximity Labeling

            Lore Gryffroy, Joren De Ryck, Veronique Jonckheere, Sofie Goormachtig, Alain Goossens, and Petra Van Damme

 

27. A Data-Driven Signaling Network Inference Approach for Phosphoproteomics

            Imani Madison, Fin Amin, Kuncheng Song, Rosangela Sozzani, and Lisa Van den Broeck

 

28. Pairwise and Multi-Chain Protein Docking Enhanced Using LZerD Web Server

            Harini Kannan, Charles Christoffer, M. Michael Gromiha, and Daisuke Kihara

 

29. Predicting Protein Interaction Sites Using PITHIA

            SeyedMohsen Hosseini and Lucian Ilie

 

30. Using PlaPPISite to Predict and Analyze Plant Protein-Protein Interaction Sites

            Jingyan Zheng, Xiaodi Yang, and Ziding Zhang

 

31. Machine Learning Methods for Virus-Host Protein-Protein Interaction Prediction

            Betül Asiye Karpuzcu, Erdem Türk, Ahmad Hassan Ibrahim, Onur Can Karabulut, and Barış Ethem Süzek

 

32. Protein-Protein Interaction Network Exploration Using Cytoscape

            Aqsa Majeed and Shahid Mukhtar

 

33. Search, Retrieve, Visualize, and Analyze Protein-Protein Interactions from Multiple Databases: A Guide for Experimental Biologists

            Vijaykumar Yogesh Muley

 

34. Centrality Analysis of Protein-Protein Interaction Networks Using R

            Vijaykumar Yogesh Muley

 

35. Protein-Protein Interaction Network Analysis Using NetworkX

            Mehadi Hasan, Nilesh Kumar, Aqsa Majeed, Aftab Ahmad, and Shahid Mukhtar

 

36. Building Protein-Protein Interaction Graph Database Using Neo4j

            Nilesh Kumar and Shahid Mukhtar