Non-Ribosomal Peptide Biosynthesis and Engineering: Methods and Protocols

ISBN-13: 9781071632130 / Angielski

Michael Burkart; Fumihiro Ishikawa

Opis

This volume provides new technologies on NRPSs and related carrier protein dependent synthases, including polyketide synthases (PKS) and fatty acid synthases (FAS). Chapters detail enzymology, structural biology, proteopromics, chemical biology, natural product chemistry, and bioinformatics. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Non-Ribosomal Peptide Biosynthesis and Engineering: Methods and Protocols aims to feature methods that will be beneficial to new researchers, and those wanting to adopt new methodologies into their research.

Spis treści

Part I Background and Overview

1. The Assembly-line Enzymology of Nonribosomal Peptide Biosynthesis

Chitose Maruyama and Yoshimitsu Hamano

 

2. Structural Studies of Modular Nonribosomal Peptide Synthetases

Ketan D. Patel, Syed Fardin Ahmed, Monica R. MacDonald, and Andrew M. Gulick

 

Part II In Vivo and In Vitro Methods

3. Using NMR Titration to Study Protein-Protein Interactions in AcpP Dependent FAS-II

Desirae A. Mellor, Javier O. Sanlley, and Michael D. Burkart

 

4. Chemoproteomic Profiling of Adenylation Domain Functions in Gramicidin S-producing Nonribosomal Peptide Synthetases

Fumihiro Ishikawa and Genzoh Tanabe

 

5. In Vitro Biochemical Characterization of Excised Macrocyclizing Thioesterase Domains from Non-Ribosomal Peptide Synthetases

Jordan T. Brazeau-Henrie, André R. Paquette, and Christopher N. Boddy

 

6. Chemo-Enzymatic Synthesis of Non-Ribosomal Macrolactams by a Penicillin-binding Protein-type Thioesterase

Masakazu Kobayashi, Kei Fujita, Kenichi Matsuda, and Toshiyuki Wakimoto

 

7. Directed Evolution of the BpsA Carrier Protein Domain for Recognition by Non-cognate 4’-Phosphopantetheinyl Transferases to Enable Inhibitor Screening

Alistair S. Brown, Jeremy G. Owen, and David F. Ackerley

 

8. Unraveling Structural Information of Multi-Domain Nonribosomal Peptide Synthetases by Using Photo-Crosslinking Analysis with Genetic Code Expansion

Julia Diecker, Wolfgang Dörner, Jennifer Rüschenbaum, and Henning D. Mootz

 

9. A Chemoenzymatic Approach to Investigate Cytochrome P450 Crosslinking in Glycopeptide Antibiotic Biosynthesis

Y. T. Candace Ho, Yongwei Zhao, Julien Tailhades, and Max J. Cryle

 

10. Cross-Linking of the Nonribosomal Peptide Synthetase Adenylation Domain with a Carrier Protein Using a Pantetheine-Type Probe

Akimasa Miyanaga, Fumitaka Kudo, and Tadashi Eguchi

 

11. A Practical Guideline to Engineering Non-Ribosomal Peptide Synthetases

Nadya Abbood, Leonard Präve, Kenan A. J. Bozhueyuek, and Helge B. Bode

 

12. Probing Substrate-Loaded Carrier Proteins by Nuclear Magnetic Resonance

Neeru Arya, Kenneth A. Marincin, and Dominique P. Frueh

 

13. Ribosomal Synthesis of Peptides Bearing Noncanonical Backbone Structures via Chemical posttranslational modifications

Yuki Goto and Hiroaki Suga

 

14. Thioester Capture Strategy for the Identification of Nonribosomal Peptide and Polyketide Intermediates

Yueying Li, Lauren A. Washburn, and Coran M. H. Watanabe

 

15. Chemical Labeling of Protein 4′-Phosphopantetheinylation in Surfactin-Producing Nonribosomal Peptide Synthetases

Fumihiro Ishikawa and Genzoh Tanabe

 

Part III: Bioinformatics methods

16. Norine: Bioinformatics Methods and Tools for the Characterization of Newly Discovered NonRibosomal Peptides

Areski Flissi, Matthieu Duban, Philippe Jacques, Valérie Leclère, and Maude Pupin