Protein termini represent a major route to protein regulation. From the moment the very first amino acid of a polypeptide chain exits the ribosome there is potential for steering from the cellular environment. This volume of Methods in Enzymology Modifications and Targeting of Protein Termini focuses on Protein N-termini and C-termini and their modifications which include acetylation, arginylation, myristoylation and oxidation. Also, the impact of terminal modifications is covered, in particular the impact on protein turnover and the ubiquitin E3 ligases which specifically recognize protein N-termini (N-degrons) and C-termini (C-degrons). In addition to the detailed methods and laboratory protocols, the chapters include informative overviews and reviews of the different subfields.
1. Title of Book - p. i 2. Cover image - p. i 3. Title page - p. ii 4. Table of Contents - p. iii 5. Series Page - p. iii 6. Copyright - p. iii 7. Contributors - p. xvii 8. Chapter One: Proteome analysis of puromycin-labeled nascent polypeptides - p. 1 9. Chapter Two: Hunter-Dia: An updated protocol for enrichment and mass spectrometry-based identification of protein N-terminal peptides - p. 25 10. Chapter Three: TermineR: Bioinformatic processing of shotgun proteomics data for the annotation and quantitation of protein termini - p. 43 11. Chapter Four: DEGRONOPEDIA: A practical guide to identifying and targeting protein degrons - p. 67 12. Chapter Five: Quantitative insights into protein turnover and ubiquitination with HiBiT and NanoBRET - p. 95 13. Chapter Six: Development of a flow cytometric method to evaluate the impact of N-terminal sequences on protein stability - p. 121 14. Chapter Seven: Generation and characterization of engineered N-degrons of the N-degron pathway using the ubiquitin-reference technique - p. 147 15. Chapter Eight: Characterization of the autophagic N-degron pathway and monitoring its chemical modulation for therapeutic development - p. 173 16. Chapter Nine: Characterization of the E3 ligase KCMF1 as a ZZ/N-recognin of the autophagic Arg/N-degron pathway - p. 211 17. Chapter Ten: Identification of the Ac/N-degron recognition domain in the MARCHF6 E3 ubiquitin ligase - p. 237 18. Chapter Eleven: Affinity purification-mass spectrometry to identify nuclear protein interactions of N-terminal acetyltransferase NAA40 - p. 259 19. Chapter Twelve: Proximity labelling of interacting proteins by TurboID - p. 283 20. Chapter Thirteen: Chemical proteomic approaches to investigate S-prenylation - p. 299 21. Chapter Fourteen: Profiling of C-terminal prenylated proteins using tandem mass tagging - p. 317 22. Chapter Fifteen: Fluorescence polarization binding assays for the E3 ligase FEM1C - p. 347
Protein termini represent a major route to protein regulation. From the moment the very first amino acid of a polypeptide chain exits the ribosome there is potential for steering from the cellular environment. This volume of Methods in Enzymology Modifications and Targeting of Protein Termini focuses on Protein N-termini and C-termini and their modifications which include acetylation, arginylation, myristoylation and oxidation. Also, the impact of terminal modifications is covered, in particular the impact on protein turnover and the ubiquitin E3 ligases which specifically recognize protein N-termini (N-degrons) and C-termini (C-degrons). In addition to the detailed methods and laboratory protocols, the chapters include informative overviews and reviews of the different subfields.
1. Title of Book - p. i 2. Cover image - p. i 3. Title page - p. ii 4. Table of Contents - p. iii 5. Series Page - p. iii 6. Copyright - p. iii 7. Contributors - p. xvii 8. Chapter One: Proteome analysis of puromycin-labeled nascent polypeptides - p. 1 9. Chapter Two: Hunter-Dia: An updated protocol for enrichment and mass spectrometry-based identification of protein N-terminal peptides - p. 25 10. Chapter Three: TermineR: Bioinformatic processing of shotgun proteomics data for the annotation and quantitation of protein termini - p. 43 11. Chapter Four: DEGRONOPEDIA: A practical guide to identifying and targeting protein degrons - p. 67 12. Chapter Five: Quantitative insights into protein turnover and ubiquitination with HiBiT and NanoBRET - p. 95 13. Chapter Six: Development of a flow cytometric method to evaluate the impact of N-terminal sequences on protein stability - p. 121 14. Chapter Seven: Generation and characterization of engineered N-degrons of the N-degron pathway using the ubiquitin-reference technique - p. 147 15. Chapter Eight: Characterization of the autophagic N-degron pathway and monitoring its chemical modulation for therapeutic development - p. 173 16. Chapter Nine: Characterization of the E3 ligase KCMF1 as a ZZ/N-recognin of the autophagic Arg/N-degron pathway - p. 211 17. Chapter Ten: Identification of the Ac/N-degron recognition domain in the MARCHF6 E3 ubiquitin ligase - p. 237 18. Chapter Eleven: Affinity purification-mass spectrometry to identify nuclear protein interactions of N-terminal acetyltransferase NAA40 - p. 259 19. Chapter Twelve: Proximity labelling of interacting proteins by TurboID - p. 283 20. Chapter Thirteen: Chemical proteomic approaches to investigate S-prenylation - p. 299 21. Chapter Fourteen: Profiling of C-terminal prenylated proteins using tandem mass tagging - p. 317 22. Chapter Fifteen: Fluorescence polarization binding assays for the E3 ligase FEM1C - p. 347
