Molecular modeling of the transmembrane domain of envelope glycoproteins from flaviviridae viruses [Elektronische Ressource] / von Siti Azma Jusoh

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Sujets

• Naturwissenschaften

Informations

• Publié par: universitat_des_saarlandes
• Publié le: 01 janvier 2010
• Nombre de lectures: 36
• Langue: Deutsch
• Poids de l'ouvrage: 3 Mo

Extrait

Molecular Modeling of
the Transmembrane Domain
of Envelope Glycoproteins from Flaviviridae
Viruses


Dissertation
zur Erlangung des Grades
des Doktors der Naturwissenschaften
der Naturwissenschaftlich-Technischen Fakultät III
Chemie, Pharmazie, Bio- und Werkstoffwissenschaften
der Universität des Saarlandes


von
Siti Azma Jusoh

Saarbrücken
November 2010


















Tag des Kolloquiums: 16. Dezember 2009
Dekan: Prof. Dr. Petra Bauer
Berichterstatter: Prof. Dr. Volkhard Helms
Prof. Dr. Richard Zimmerman
Akad. Mitarbeiter: Dr. Michael Hutter



i















ii















Hiermit versichere ich an Eides statt, dass ich die vorliegende Arbeit selbständig und ohne Benutzung
anderer als der angegebenen Hilfsmittel angefertigt habe. Die aus anderen Quellen oder indirekt
übernommenen Daten und Konsepte sind unter Angabe der Quelle gekennzeichnet. Die Arbeit wurde
bisher weder In- noch im Ausland in gleicher oder ähnlicher Form in einem Verfahren zur Erlangung
eines akademischen Grades vorgelegt.


Saarbrücken, Dezember 2010
iii Acknowledgement
Foremost, I owe my deepest gratitude to my supervisor, Prof. Dr. Volkhard Helms for accepting me as
his student and guiding me along my PhD journey. Thank you for patiently editing my writing and
giving many useful advices. I also would like to thank his wife, Regina who helped my family and me
during our initial stage in Germany. I would like to thank the group secretary, Kerstin for helping me
with the paperworks.

I am thankful to the group members of Computational Biology Group for sharing memorable
moments, experiences, valuable academic discussion as well as many other aspects of life especially Dr.
Michael Hutter, Dr. Tihamér Geyer, Dr. Wei Gu, Mazen Ahmad, Peter Walter, Dr. Susanne Eyrisch,
Mohamed Hamed Ali Fahmy, Christian Spaniol, Jennifer Metzger, Nadine Schaadt and Po-Hsien Lee.

My special appreciation goes to Barbara Hutter, Özlem Ulucan, Yvonne and Alesandro Marangon for
being my closest friends.

I will not forget to thank Dr. Shirley Siu and Prof. Dr. Rainer Böckmann for teaching me MD
simulations in membrane lipid bilayer. I thank Danielle, Caroline and Beate from Prof. Dr. Rainer
Böckmann group and many other friends in Germany for various kinds of help.

I thank Dr. Christoph Welsch from the Johann Wolfgang Goethe University, Frankfurt for his
contributions to the project described in Chapter 3. His contributions are marked specifically in the text.

I would not have been able to perform my study without financial contribution from my main sponsor,
the Universiti Teknologi MARA Malaysia, and additional financial supports from the Volkswagen
Foundation. I would like to acknowledge Centre for Bioinformatics of Saarland University for the
computational and research supports.

Finally, I would like to thank my parents, Jusoh Ismail and Aini Mohamud for their love, care and
dedication to rise me. I am grateful for my beloved husband, Mustakim Mohamed Adnan for his
endless love and continuous support and also both of my sons Luqman Syahmi and Ayman Shafi for
being the major drive that motivates me every single day. Thank you for my families for always being
there for me.

I thank to Allah SWT for His bless and guidance through this entire journey.

iv

Abstract

The putative transmembrane (TM) domains of the envelope glycoproteins from the family Flaviviridae
consist of a highly polar segment in between two hydrophobic stretches. This type of sequence pattern
does not yet exist in the database of high resolution structures of membrane proteins. Mutagenesis
studies have shown that the TM domains act as membrane and signal anchors, and are responsible for
heterodimerization. In hepatitis C virus (HCV), the TM domains of the envelope glycoproteins E1 and
E2 were hypothesized to heterodimerize via an ion pair of Lys-Asp. Our MD simulations showed that
the E1-E2 heterodimer formed by the charged residues located in the core of the lipid bilayer stabilized
the helical conformation of E2. We compared the effect of other types of ion pair interactions using
engineered peptides and obtained similar results. We found that an Asp amino acid had the strongest
kink-inducing effect on the helix when it was located in the middle of a single-pass TM helix. The
extended analyses on dengue, Japanese encephalitis, West Nile and bovine viral diarrhea viruses again
showed that their putative TM domains behave similarly. All the TM domains of the E1/prM tended to
tilt and remain helical in membrane bilayer. In contrast, the TM domains of the E2/E that contain a
central Asp residue were severely kinked. Altogether, these TM domains illustrated a similar structural
behavior in the lipid bilayer milieu.

v Kurzfassung

Die mutmaßlichen Transmembran (TM)-Domänen der Hüllglykoproteine der Familie Flaviviridae
bestehen aus einem hochpolaren Segment zwischen zwei hydrophilen Abschnitten. Diess
Sequenzmuster sind noch nicht in der Datenbank hochaufgelöster Strukturen von Membranproteinen
enthalten. Gemäß Mutagenesestudien agieren die TM-Domänen als Membran- und Signalanker und
sind für die Heterodimerisierung verantwortlich. Im Hepatitis C-Virus (HCV) heterodimerisieren die
TM-Domänen der Hüllglykoproteine E1 und E2 möglicherweise über ein Ionenpaar zwischen Lys-Asp.
Unsere MD-Simulationen zeigten, dass das E1-E2-Dimer, das durch die geladenen Residuen im Kern
der Lipiddoppelschicht gebildet wird, die helikale Konformation von E2 stabilisiert. Der Effekt anderer
Ionenpaarinteraktionen in künstlichen Peptiden führte zu ähnlichen Ergebnissen. Asp in der Mitte einer
TM-Helix verursachte den stärksten Krümmungseffekt. Weitere Analysen mit anderen Flaviviridae
(Dengue, Japanese encephalitis, West Nile und bovine viral diarrhea virus) zeigten ebenfalls ein
ähnliches Verhalten ihrer mutmaßlichen TM-Domänen. Alle TM-Domänen von E1/prM tendierten zur
Krümmung und blieben in der Membrandoppelschicht helikal. Hingegen waren die TM-Domänen von
E2/E, die ein zentrales Asp enthalten, stark gekrümmt. Insgesamt zeigten diese mutmaßlichen TM-
Domänen ein ähnliches strukturelles Verhalten in der Membran.
vi
Thesis Overview

This thesis deals with the transmembrane (TM) helix segments of the two envelope glycoproteins from
Flaviviridae viruses which contain several highly polar amino acid residues located in the centre of the
TM segments. Here, the structure of the thesis is outlined.
Chapter 1 provides a brief introduction of membrane proteins which covers their types, structure and
functions, purposely to highlight their crucial roles in living organisms. Then, I specifically explain the
mechanisms and components related to the synthesis of the helical membrane proteins. The ribosome-
translocon complexes are shown to directly be involved in the biogenesis, the lateral translocation into
the membrane lipids and the topological decision of the membrane proteins. Furthermore, I bring up the
unresolved issues about the models of the active ribosome-translocon complexes and recent discussions
regarding the controversial biological hydrophobicity scale. These fundamental issues are critical in the
decision making to produce accurate prediction methods for membrane proteins. In addition, I give
some information about the membrane lipids which are the residing home for the membrane proteins
and their dynamic properties as well as their interaction to each other. At the end, I summarized the
background of the peptides that were used in this thesis.
In Chapter 2, the technique of classical MD simulation is briefly explained including a discussion of the
utilized force field. The protocols to implement a simulation of a peptide in lipid bilayer system are also
described here. Some experimental data are shown side by side with respective results from other
simulation studies.
Chapter 3 presents the results of our first project with the objective to study an ion pair interaction that
mediates a TM helix dimer. This project was motivated by the abundant experimental data on hepatitis
C virus (HCV) that suggested an important contribution of a salt-bridge for the dimerization of the
putative TM helices from the E1 and E2 envelope glycoproteins. We modeled the suggested E1-E2
heterodimer with the Lys-Asp salt-bridge purposely to observe the effect on the helical structure. We
explored with the MD simulation methods other possibilities that can weaken or strengthen the helix-
helix interaction by performing mutations on the selected key residues as proposed by the experiments.
From this, we conclude that the strong E1-E2 dimer interaction is driven by the ion pair. But the ion
pa