Understanding antibiotic permeation through OccD3 of Pseudomonas aeruginosa

81 Pages·2017·1.61 MB·English

Understanding antibiotic permeation through
OccD3 of Pseudomonas aeruginosa

by

Gowrishankar Soundararajan

a thesis submitted in partial fulfillment
of the requirements for the degree of

Doctor of Philosophy
in Biochemical Engineering

Approved Dissertation Committee

Prof. Dr. Mathias Winterhalter
Jacobs University, Bremen

Prof. Dr. Richard Wagner
Jacobs University, Bremen

Dr. Björn Windshügel
Fraunhofer IME, Hamburg

Date of Defense: 28th June 2017
Department of Life Science and Chemistry

1
2
Statutory Declaration
(Declaration on Authorship of a Dissertation)

I, Gowrishankar Soundararajan hereby declare, under penalty of perjury,
that I am aware of the consequences of a deliberately or negligently wrongly
submitted affidavit, in particular the punitive provisions of § 156 and § 161
of the Criminal Code (up to 1 year imprisonment or a fine at delivering a
negligent or 3 years or a fine at a knowingly false affidavit).

Furthermore I declare that I have written this PhD thesis independently,
unless where clearly stated otherwise. I have used only the sources, the data
and the support that I have clearly mentioned.

This PhD thesis has not been submitted for the conferral of a degree
elsewhere.

Bremen 29 -6-2017
Place Date

Signature

3
4
Dedicated to my Parents, my Sister and Sadhguru

5
6
Acknowledgements:
First of all I would like to thank Prof. Mathias Winterhalter for giving
me this opportunity to do PhD in his lab. Though I was from a different
background, he gave me a chance to work in this interesting field of
Biophysics. I also thank him for giving me the time and latitude to work on
ideas during my PhD and also for his poise during most situations of my
study.
I would like to thank Prof. Roland Benz, Prof. Ullrich Kleinekathofer,
Prof. Richard Wagner and Dr. Bjorn Windshugel for being part of my PhD
proposal committee.
I also thank the ‘TRANSLOCATION’ consortium, the ‘Innovative
Medicines Joint Unit’, for providing me the funding during my PhD tenure.
I thank all my colleagues and lab members, especially Satya for
collaborating with me on my projects and Naresh for being there as a moral
support from the beginning. I thank my other colleagues Dr. Daniel, Ishan,
Funda, Dr. Ivan, Dr. Farhan, Dr. Sonalli, Dr. Alex, Dr. Remi, Harsha, Dr.
Jules, Lorraine, Eva, Jayesh, Frank, Dr. Koldo, Dr. Tatiana and Vinay from
Dr. Kleinekathofer group for the times we shared together.
7
I would like to thank my friends in Germany who are like my second
family viz, Dinesh, Anandhi, Akshaya, Ram, Hari, Simone, Satya, Bhargav
and all my other friends from Isha.
I dedicate this thesis to my parents; my Mother and my Father who
have known life with me as only giving and never expected anything back
from my selfish self. I also dedicate my thesis to my sweet sister Abi, for I
am only lucky to have her in my life. And I finally dedicate this work to my
Guru, Sadhguru; my very breath every moment of my life. Shambho.
“One moment of gratitude can transform your whole life” - Sadhguru

8
Table of Contents
Abstract………………………………………………………………….11
Part 1: Introduction
1.1 Introduction to the field…………………………………………….....15
1.2 Mechanism of antibiotic resistance in Gram negative Bacteria……....18
1.3 Antibiotic resistance in Pseudomonas aeruginosa……………………23
1.4 Outer membrane of Pseudomonas aeruginosa………………………..27
1.5 References……………………………………………………………..31
1.6 Scope of the thesis………………………………………………….….40
Part 2: Antibiotic translocation through the Outer membrane channel
OccD3 of Pseudomonas aeruginosa.
2.1 Summary………………………………………………………………44
2.2 Understanding Carbapenem translocation through OccD3 of
Pseudomonas aeruginosa…………………………………………………..45
Part 3: Annex
3.1 Molecular blocking of antibiotics through bacterial OmpC porin by
selective chemical protein modification……………………………………66
Part 4: Conclusion and future outlook……………………………………...92
Publications………………………………………………………………...95

9
10