Bacterial Multidrug Exporters: Methods and Protocols

ISBN-13: 9781493984909 / Angielski / Miękka / 2018 / 355 str.

Akihito Yamaguchi; Kunihiko Nishino

Spis treści

Part I: Structural Analysis of Bacterial Multidrug Exporters

 

1. High Resolution Crystallographic Analysis of AcrB Using Designed Ankyrin Repeat Proteins (DARPins)

            Heng Keat Tam, Viveka Nand Malviya, and Klaas M. Pos

 

2. Crystallographic Analysis of Drug and Inhibitor-Binding Structure of RND-Type Multidrug Exporter AcrB in Physiologically-Relevant Asymmetric Crystals

            Ryosuke Nakashima, Keisuke Sakurai, and Akihito Yamaguchi

 

3. Crystallographic Analysis of MATE-Type Multidrug Exporter with Its Inhibitors

            Tsukasa Kusakizako, Yoshiki Tanaka, Christopher J. Hipolito, Hiroaki Suga, and Osamu Nureki

 

4. Crystallographic Analysis of the CusBA Heavy-Me

tal Efflux Complex of Escherichia coli

            Jared A. Delmar and Edward W. Yu

 

5. Purification of AcrAB-TolC Multidrug Efflux Pump for Cryo-EM Analysis

            Dijun Du, Zhao Wang, Wah Chiu, and Ben F. Luisi

 

6. NMR Spectroscopy Approach to Study the Structure, Orientation, and Mechanism of the Multidrug Exporter EmrE

            Maureen Leninger and Nathaniel J. Traaseth

 

7. Generation of Conformation-Specific Antibody Fragments for Crystallization of the Multidrug Resistance Transporter MdfA

            Frank Jaenecke, Yoshiko Nakada-Nakura, Kumar Nagarathinam, Satoshi Ogasawara, Kehong Liu, Yunhon Hotta, So Iwata, Nor

imichi Nomura, and Mikio Tanabe

 

Part II: Biochemical and Bioengineering Analysis of Bacterial Multidrug Exporters

 

8. Biochemical Reconstitution and Characterization of Multi-Component Drug Efflux Transporters

            Martin Picard, Elena B. Tikhonova, Isabelle Broutin, Shuo Lu, Alice Verchère, and Helen I. Zgurskaya

 

9. Covalently Linked Trimers of RND (Resistance-Nodulation-Division) Efflux Transporters to Study Their Mechanism of Action: Escherichia coli AcrB Multidrug Exporter as an Example

            Hiroshi Nikaido

 

10. Determining Ligand Path through a Major Drug Transporter, AcrB, in Escherichia coli

            Fasahath Husain and Hiroshi Nikaido

 

Part III: Computational Analysis of Bacterial Multidrug Exporters

 

11. Molecular Modeling of Multi-Drug Properties of Resistance Nodulation Division (RND) Transporters

            Pierpaolo Cacciotto, V. K. Ramaswamy, Giuliano Malloci, Paolo Ruggerone, and Attilio V. Vargiu

 

12. A Transcriptomic Approach to Identify Novel Drug Efflux Pumps in Bacteria

            Liping Li, Sasha G. Tetu, Ian T. Paulsen, and Karl A. Hassan

 

Part IV: Biomedical Approach for Bacterial Multidrug Exporters

 

13. Regulation of the Expression of Bacterial Multidrug Exporters by Two-Component Signal Transduction Systems

            Kunihiko Nishino

 

14. Study of the Expression of Bacterial Multidrug Efflux Pumps in Anaerobic Conditions

            Jingjing Sun, Ziqing Deng, Danny Ka Chun Fung, and Aixin Yan

 

15. Identification of a Staphylococcus aureus Efflux Pump Regulator Using a DNA-Protein Affinity Technique

            Que Chi Truong-Bolduc and David C. Hooper

 

16. High Throughput Flow Cytometry Screening of Multidrug Efflux Systems

            Mark K. Haynes, Matthew Garcia, Ryan Peters, Anna Waller, Pietro Tedesco, Oleg Ursu, Cristian G. Bologa, Radleigh G. Santos, Clemencia Pinilla, Terry H. Wu, Julie A. Lovchik, Tudor I. Oprea, Larry A. Sklar, and George P. Tegos

 

Part V: Advanced Technologies Expected for Application to Multi

drug Efflux Transport Studies

 

17. Single-Molecule Analysis of Membrane Transporter Activity by Means of a Microsystem

            Rikiya Watanabe, Naoki Soga, Shin-ya Ohdate, and Hiroyuki Noji

 

18. Large Scale Femtoliter Droplet Array for Single Cell Efflux Assay of Bacteria

            Ryota Iino, Shouichi Sakakihara, Yoshimi Matsumoto, and Kunihiko Nishino

 

19. Reconstitution and Transport Analysis of Eukaryotic Transporters in the Post-Genomic Era

            Hiroshi Omote and Yoshinori Moriyama

Blurb

This detailed volume utilizes our current understanding of the structural basis of multidrug recognition and multidrug efflux mechanisms to provide protocols involving these vital intrinsic membrane proteins widely distributed in bacteria. Beginning with protocols for the structural analysis of bacterial multidrug exporters, the book continues with sections on biochemical and bioengineering analysis, computational analysis, biomedical approaches, as well as advanced technologies expected to be applied to multidrug efflux transport studies. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective chapters, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and practical, Bacterial Multidrug Exporters: Methods and Protocols serves as an ideal guide to

this fast moving field of study.