Computational Insights into the Antimicrobial Mechanism of Action of Class II Bacteriocins.

148 Pages·2017·6.62 MB·English

Computational Insights into the
Antimicrobial Mechanism of Action of
Class II Bacteriocins.

A DISSERTATION SUBMITTED TO THE FACULTY OF THE GRADUATE SCHOOL OF
THE UNIVERSITY OF MINNESOTA
BY
PANAGIOTA KYRIAKOU

IN PARTIAL FULLFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF
DOCTOR OF PHILOSOPHY.

YIANNIS KAZNESSIS, ADVISOR

MAY 2017
© Panagiota Kyriakou 2017
Acknowledgments
First, and foremost, thank you to my Advisor, Professor Yiannis Kaznessis, for
giving me the opportunity to join his group and for his continuous support during my
doctoral studies. Whether I had a question about research or my career, Yiannis’s door
was always open. The skills and knowledge I gained from working in the Kaznessis
group will stay with me in all my future endeavors.
I am grateful to Prodromos Daoutidis, Joseph Zasadzinski, and Jonathan Sachs for
their willingness to serve as my committee members and for their brilliant comments,
suggestions, and advice. I also want to thank our collaborators in the Nissen-Meyer
group at the University of Oslo, especially Dr. Per E. Kristiansen, for providing much-
needed experimental insight into my work.
I would like to acknowledge the support of my current and previous groupmates in
the Kaznessis group, particularly Brittany Forkus and Michael Vlysidis, who go far
beyond being just colleagues and groupmates. Their support and friendship was
indispensable throughout my studies. I would like to extend my thanks to all the people
in CEMS who were a part of my life these past five years.
I was lucky to meet people who not only made my stay in Minneapolis enjoyable,
but also contributed to my development as a person. Angelika, Sofia, and Smaro created
a feeling of family for me here and I am eternally thankful for that. Moreover, I am
grateful to the entire Greek community in Minneapolis, and to my friends back in Greece,
for their tireless support. Special thanks to my close friend, Stavroula, who stayed with
me in Minneapolis for three months to help me through a challenging time.
Finally, I would like to express my immense gratitude to my parents, my brother,
and the rest of my family for the love and endless support with which they surround me.
They were with me through every step, every challenge, and every success. Finally, I
would like to thank my partner, Tyler, for making my life happier the last two years. His
genuine support, love, and encouragement played a key role in achieving my goals.

i
To my family

ii
Abstract
Antibiotic resistance is a global problem and poses an alarming threat to public
health. Microorganisms resistant to all commercially available antibiotics have emerged,
undermining the ability to fight infectious diseases. The antibiotic resistance crisis has
been attributed to the overuse of antibiotics, as well as a lack of new drug development.
Coordinated efforts are needed to overcome this challenge, including discovery of
alternative drugs.
Bacteriocins are bacteria-produced, antimicrobial peptides that are potentially
powerful antibiotic drug candidates. Despite considerable scientific interest around
bacteriocins, and despite their promise as potent, latent antibiotics, their everyday
medical value has been negligible. In order to more effectively utilize the full potential of
bacteriocins as a platform to develop new antibacterial agents, a detailed understanding
of their mechanism of action is required. This mechanistic insight will offer ways to
control and optimize their activity and selectivity against specific pathogens, greatly
enhancing their potential for medical applications. The goal of this work is to elucidate
the mechanism of action of class II bacteriocins by employing a variety of computational
methods that are built around atomistic molecular dynamics simulations.
First, we studied Plantaricin EF, a two-peptide class IIb bacteriocin. This bacteriocin
was simulated in different environments including water, micelles, and lipid bilayers. The
interaction between the two peptides that promotes dimerization, and the interaction
between the dimer and the membrane were elucidated. Guided by experimental studies,
a transmembrane model of the dimer embedded in the bilayer was additionally
designed. Results obtained from a 1 μs long atomistic molecular dynamics simulation,
demonstrated for the first time that a bacteriocin, with a narrow antimicrobial activity
range, can by itself form a water (and potentially ion) permeable, toroidal pore in a lipid
bilayer. This pore was characterized in detail.
It is not unlikely that the mechanism of action of bacteriocins can involve poration of
the membrane as well as receptor-mediation. Therefore, the interaction of a bacteriocin
with its putative receptor was also examined. Lacking the structure of a receptor, we
employed structure-prediction techniques in combination with docking calculations, and
iii
molecular dynamics simulations. For the first time a class II bacteriocin-receptor complex
was built, setting the ground for investigating the role that receptors play in the
bactericidal activity of these antimicrobial peptides.
We believe that our findings could be of importance to the designing of new
antibiotic agents, as it would guide the search for better bacteriocins toward peptides
with improved activity and specificity, that form stable pores, increase water or ion
permeability, and interact more efficiently with a receptor.

iv
Table of Contents
ACKNOWLEDGMENTS ............................................................................................................................................. I
ABSTRACT .......................................................................................................................................................... III
TABLE OF CONTENTS ............................................................................................................................................. V
LIST OF FIGURES ................................................................................................................................................ VIII
LIST OF TABLES .................................................................................................................................................... X
ABBREVIATIONS .................................................................................................................................................. XI
CHAPTER 1 INTRODUCTION ..................................................................................................................... 1
1.1. ANTIBIOTIC RESISTANCE (AMR) ON THE RISE ................................................................................................ 1
1.2. ANTIMICROBIAL PEPTIDES (AMPS) AS A SOLUTION ........................................................................................ 3
1.2.1. Possible mechanism of action (MOA) of AMPs ............................................................. 4
1.3. BACTERIOCINS: AN INTERESTING GROUP OF AMPS ........................................................................................ 7
1.3.1. Categories of bacteriocins produced by lactic acid bacteria (LAB) ............................... 8
1.4. MOLECULAR SIMULATION OF BACTERIOCINS .............................................................................................. 14
1.4.1. Theory on Molecular Dynamics (MD) Simulations ..................................................... 14
1.4.2. Previous MD on bacteriocins ...................................................................................... 16
1.5. THESIS OVERVIEW ................................................................................................................................. 17
CHAPTER 2 SIMULATION OF A CLASS IIB BACTERIOCIN IN WATER AND ON MICELLES ........................... 20
2.1. INTRODUCTION ..................................................................................................................................... 20
2.2. MATERIALS AND METHODS...................................................................................................................... 23
2.3. RESULTS AND DISCUSSION ...................................................................................................................... 25
2.3.1. Simulation of individual peptides in water ................................................................. 25
2.3.2. Simulation of proposed dimers in water ..................................................................... 27
2.3.3. Simulation of the individual peptides in the presence of DPC micelles ....................... 29
2.4. CONCLUSIONS ...................................................................................................................................... 32
CHAPTER 3 BEHAVIOR OF A CLASS IIB BACTERIOCIN AND ITS MUTANTS ON THE SURFACE OF A MODEL
LIPID BILAYER ......................................................................................................................................... 33
3.1. INTRODUCTION ..................................................................................................................................... 33
3.2. MATERIALS AND METHODS...................................................................................................................... 35
3.2.1. Simulation Methods and Parameters ......................................................................... 35
v
3.2.2. Atomistic model of PlnEF, and a membrane............................................................... 36
3.2.3. Positioning of the peptides on the surface of the membrane .................................... 36
3.2.4. Bacteriocin activity assay ........................................................................................... 37
3.3. RESULTS AND DISCUSSION ...................................................................................................................... 37
3.3.1. Experimental antimicrobial activity ............................................................................ 37
3.3.2. Simulation of the wild type bacteriocin PlnEF ............................................................ 40
3.3.3. Simulation of dimers of PlnE and PlnF that contain single amino acid substitutions . 47
3.3.4. Connection of simulated biophysical interactions with the experimental activity ..... 52
3.4. CONCLUSIONS ...................................................................................................................................... 53
CHAPTER 4 DESIGNING THE STRUCTURE OF A TRANSMEMBRANE CLASS IIB DIMER .............................. 55
4.1. INTRODUCTION ..................................................................................................................................... 55
4.2. MATERIALS AND METHODS...................................................................................................................... 56
4.2.1. Experimental methods ................................................................................................ 56
4.2.2. Building the Dimer Model ........................................................................................... 56
4.2.3. Molecular Dynamics (MD) Simulation Methods and Parameters .............................. 57
4.3. RESULTS AND DISCUSSION ...................................................................................................................... 58
4.3.1. Model of Plantaricin EF inserted into membrane bilayer based on mutational assays
and the known NMR structures of the individual peptides ................................................................... 58
4.3.2. Molecular dynamics (MD) simulation and evaluation of the membrane-inserted
model of Plantaricin EF ......................................................................................................................... 59
4.4. CONCLUSIONS ...................................................................................................................................... 65
CHAPTER 5 COULD CLASS IIB BACTERIOCINS INDUCE PORE FORMATION? ............................................ 67
5.1. MATERIALS AND METHODS...................................................................................................................... 68
5.1.1. System components .................................................................................................... 68
5.1.2. Molecular dynamics ................................................................................................... 69
5.2. RESULTS .............................................................................................................................................. 70
5.2.1. Structural analysis of the peptides ............................................................................. 71
5.2.2. Intramolecular interactions ........................................................................................ 73
5.2.3. Membrane behavior around PlnEF ............................................................................. 75
5.2.4. Behavior of ions near the dimer ................................................................................. 79
5.2.5. Water permeability through the pore ........................................................................ 81
5.3. DISCUSSION ......................................................................................................................................... 83
vi
5.4. CONCLUSIONS ...................................................................................................................................... 89
CHAPTER 6 A FIRST LOOK AT A CLASS II BACTERIOCIN-RECEPTOR COMPLEX ......................................... 91
6.1. INTRODUCTION ..................................................................................................................................... 91
6.2. COMPUTATIONAL PROTEIN STRUCTURE PREDICTION ..................................................................................... 92
6.3. LSBB, A CLASS IID BACTERIOCIN AND ITS HYPOTHESIZED RECEPTOR, THE ZN METALLOPEPTIDASE YVJB ................... 94
6.4. METHODS ............................................................................................................................................ 97
6.4.1. Topology recognition and structure protein prediction .............................................. 97
6.4.2. Design of the Transmembrane YvjB models .............................................................. 97
T
6.4.3. Design of the surface LsbB model ............................................................................... 98
6.4.4. Molecular dynamics and docking ............................................................................... 99
6.5. RESULTS AND DISCUSSION ...................................................................................................................... 99
6.5.1. Topology and structure prediction of YvjB ............................................................... 100
6.5.2. MD simulations and docking ................................................................................... 104
6.6. CONCLUSIONS AND FUTURE DIRECTIONS .................................................................................................. 106
CHAPTER 7 SUMMARY AND CONCLUDING REMARKS .......................................................................... 108
REFERENCES .................................................................................................................................................... 112
APPENDIX .......................................................................................................................................... 124

vii
List of Figures
Figure 1-1: Possible mechanisms of action of membrane active AMPs .......................... 5
Figure 1-2: Suggested Mechanism of Action of Microcin J25 ......................................... 6
Figure 1-3: Proposed MOA of class IIa bacteriocins .....................................................10
Figure 1-4: The GxxxG motif ........................................................................................12
Figure 1-5: “Huge Toroidal Pore (HTP)” model of Lacticin Q .........................................13
Figure 2-1: Microscopy images of cells treated with PlnEF ............................................21
Figure 2-2: 3-D structure of Plantaricin E and F .............................................................23
Figure 2-3: Possible models of the PlnEF ......................................................................24
Figure 2-4: Dihedral angles and Energy analysis for the individual peptides in aqueous
solution .......................................................................................................26
Figure 2-5: Final snapshots of the simulation of individual peptides in water .................27
Figure 2-6: Dihedral angles and energy analysis for the proposed complexes in aqueous
solution .......................................................................................................28
Figure 2-7: Definition of the different Peptide-micelle systems .......................................30
Figure 2-8: Snapshots of systems Es1 and Es2 ............................................................31
Figure 2-9: Center of mass the peptides with respect to the micelle ..............................31
Figure 3-1: Possible steps of the MOA of PlnEF ............................................................35
Figure 3-2: Snapshots from simulations of the wild type peptides ..................................39
Figure 3-3: RMSD analysis ............................................................................................40
Figure 3-4: Structural analysis of wild type PlnEF ..........................................................41
Figure 3-5: Serine contribution to multiple hydrogen bonds ...........................................42
Figure 3-6: Distance of the wild-type peptides from the membrane center .....................43
Figure 3-7: Membrane – peptide interactions ................................................................44
Figure 3-8: Membrane deformation ...............................................................................45
Figure 3-9: The behavior of possible GxxxG motifs .......................................................46
Figure 3-10: Snapshot of the systems with mutant peptides ..........................................48
viii