RANDOM MUTAGENESIS OF NS1 PROTEIN OF INFLUENZA A H1N1 AND DOCKING OF RNA APTAMERS TO WILD TYPE AND MUTANT NS1 PROTEINS KUMUTHA CHELLIAH A dissertation submitted in partial fulfillment of the requirements for the award of the degree of Master of Science (Biotechnology) Faculty of Biosciences and Bioengineering Universiti Teknologi Malaysia JULY 2012
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RANDOM MUTAGENESIS OF NS1 PROTEIN OF INFLUENZA A H1N1 AND
DOCKING OF RNA APTAMERS TO WILD TYPE AND MUTANT NS1
PROTEINS
KUMUTHA CHELLIAH
A dissertation submitted in partial fulfillment of the
requirements for the award of the degree of
Master of Science (Biotechnology)
Faculty of Biosciences and Bioengineering
Universiti Teknologi Malaysia
JULY 2012
iv
To my dearest family and friends,
who gave me inspiration and endless support
all along.
Thank you.
v
ACKNOWLEDGEMENTS
I wish to extend my sincere gratitude to my supervisor, Dr. Chan Giek Far for
sparing her time and energy in guiding me throughout my project. She drives me to
work independently, pushes me to be more hardworking and I appreciate whatever
advice she have given me. I am privileged to have her as my supervisor because she
is an inspiration which greatly improved my thinking skills and knowledge.
I also wish to thank the staffs of Microbiology and Molecular Laboratory in
Faculty of Biosciences and Bioengineering for providing me their special assistance
and relevant facilities throughout my work. I sincerely thank Dr. Shahir Shamsir and
his staffs in Bioinformatics Laboratory for sharing their expertise and guiding me in
terms of extensive biocomputational work.
I would like to thank my peers for their continual support and tips when I
faced difficulties in my project. Their kindness is very much appreciated.
Last but not least, my family members are my pillars of strength and support.
I would like to thank them for their moral support and advice which helped me to
face the challenges in my research.
vi
ABSTRACT
The NS1A protein is a non-structural protein from influenza A virus H1N1
strain. The protein is a multifunctional protein which is capable of blocking the
defense mechanism of host immune by inhibiting the secretion of host cell IFN α/β.
Even existing vaccines cannot protect host cells against this viral infection due to
constant mutations of NS1A protein. In this study, the NS1A gene which was
formerly cloned in pET 32c(+) vector was successfully mutated using error-prone
PCR with increased concentration of MgCl2 to 10 mM and subsequently cloned into
yT&A vector and transformed into E. coli DH5α. There were four proteins that
contain non-conservative mutations from sequencing which were NS1 F103LN209D,
NS1 S7P, NS1 T76I and NS1 E159G mutant proteins. These proteins together with
the wild-type protein were modeled using EasyModeller 2.1 and were energy
minimized using GROMACS. The qualities of the structures were validated using
ERRAT, PROCHECK, Verify3D and ProSA web. All the structures were of good
quality and the high RMSD value shows that the mutant proteins have low structural
homology to the wild-type protein. This proves that the structures were affected by
point mutations. None of the mutations fell into ‘hot spot’ mutations. These proteins
were subsequently docked to RNA aptamers via HEX server to analyze the binding
regions and binding affinity of aptamers to proteins. The results obtained shows that
the protein mutations affect the binding properties of aptamers to the mutant proteins
because aptamers were docked at various regions with different binding affinities.
The aptamers with the highest binding affinity towards wild-type NS1A protein and
mutant proteins were selected which were aptamers 21, 174 and 176. These results
were expected to be useful for potential drug design to curb future H1N1 viral
infections.
vii
ABSTRAK
Protein NS1A merupakan protein nonstruktural dari virus influenza A H1N1.
Protein ini ialah protein multifungsi yang boleh menghalang mekanisma pertahanan
sel hos dengan menyekat penghasilan IFN α/β. Vaksin yang sedia ada tidak boleh
melindungi sel-sel terhadap jangkitan virus sebab protein NS1A ini sentiasa melalui
mutasi berterusan. Dalam kajian ini, gen NS1A yang diklon dalam vektor PET 32c
(+), telah berjaya dimutasikan menggunakan error-prone PCR dengan meningkatkan
kepekatan MgCl2 kepada 10 mM dan seterusnya diklonkan ke dalam vektor y T&A
dan ditransformasikan ke dalam E. coli DH5α. Terdapat empat protein yang
mengandungi mutasi bukan-konservatif dari analisa sequencing iaitu NS1
F103LN209D, S7P NS1, NS1 T76I dan NS1 E159G protein mutan. Protein ini
bersama dengan protein wild-type telah dimodelkan menggunakan EasyModeller 2.1
dan tenaga telah dikurangkan menggunakan GROMACS. Struktur kualiti protein-
protein telah disahkan dengan menggunakan ERRAT, PROCHECK, Verify3D dan
Prosa web. Semua struktur protein adalah berkualiti tinggi dan nilai RMSD yang
tinggi menunjukkan bahawa protein-protein mutan mempunyai struktur homologi
yang rendah terhadap protein wild-type. Ini membuktikan bahawa struktur protein
dipengaruhi oleh point mutation. Tiada mutasi dikenalpasti sebagai mutasi 'hot spot'.
Seterusnya, docking antara protein dan aptamer-aptamer RNA dilakukan melalui
HEX server untuk menganalisis kawasan docking dan afiniti dock aptamer-aptamer
kepada protein. Keputusan menunjukkan bahawa mutasi protein mempengaruhi
docking antara aptamer-aptamer dan protein-protein mutan kerana aptamer-aptamer
telah dock di pelbagai kawasan dengan kekuatan docking berbeza. Aptamer-aptamer
yang dock kepada protein wild-type NS1A dan protein-protein mutan dengan afiniti
paling tinggi telah dipilih iaitu aptamer 21, 174 dan 176. Keputusan ini dijangka
berguna bagi rekabentuk ubat yang berpotensi untuk mencegah jangkitan virus H1N1
masa depan.
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TABLE OF CONTENTS
CHAPTER TITLE PAGE
TITLE i
SUPERVISOR’S DECLARATION ii
DECLARATION iii
DEDICATION iv
ACKNOWLEDGEMENTS v
ABSTRACT vi
ABSTRAK vii
TABLE OF CONTENTS viii
LIST OF TABLES xi
LIST OF FIGURES xii
LIST OF ABBREVIATIONS xv
LIST OF APPENDICES xix
1 INTRODUCTION
1.1 Background of Study 1
1.2 Problem Statement 2
1.3 Research Objectives 3
1.4 Research Scope 3
1.5 Research Significance 4
ix
2 LITERATURE REVIEW
2.1 Influenza A Viruses 5
2.1.1 Evolutionary Process of Influenza A Viruses 5
2.1.2 Influenza A Virus: Structure and Function 6
2.1.3 Influenza A H1N1 2009 11
2.2 NS1 Protein 12
2.2.1 NS1A RNA Binding Domain 16
2.2.2 Effects of NS1A Gene Variation on
Structure and Function 17
2.3 Directed Evolution 18
2.3.1 Error-prone PCR 19
2.4 Bioinformatics Application 21
2.4.1 Protein Modeling 21
2.4.1.1 Comparative Protein Modeling 23
2.4.2 Protein Model Validation Tools 26
2.5 Nucleic Acid Aptamers 27
2.5.1 Advantage of Aptamers over Antibodies 28
2.5.2 Aptamers as Antiviral Drugs 29
3 MATERIALS AND METHODS
3.1 Experimental Design 31
3.2 Preparation of Luria-Bertani (LB) Broth and Agar 31
3.3 Culturing of Recombinant E. coli and Plasmid Extraction 32
3.4 Random Mutagenesis using Error-prone PCR 33
3.5 Separation of Bands using Gel Electrophoresis 34
3.6 Cloning and Transformation 35
3.6.1 Cloning of Mutated Genes into yT&A Vector 35
3.6.2 Transformation of Recombinant Plasmids into
E. coli DH5α 36
3.6.3 Screening for Clones with the Desired Inserts 37
3.7 Analysis of Mutants using Bioinformatics Tools 38
3.7.1 Sequence Analysis 38
3.7.2 Comparative Protein Modeling 39
x
3.7.3 Protein Validation 39
3.7.4 Molecular Docking 40
4 RESULTS AND DISCUSSION
4.1 Error-prone PCR 41
4.1.1 Error prone PCR with Various Concentrations of
MgCl2 42
4.1.2 Error-prone PCR with Various Concentrations of
MnCl2 43
4.1.3 Error-prone PCR with Increased Number of Cycles 45
4.2 Cloning and Colony Screening 46
4.3 Multiple Sequence Alignment 50
4.4 Comparative Protein Modeling of NS1 Protein and Structure
Analysis 57
4.5 Model Quality Validation 59
4.5.1 ERRAT 60
4.5.2 PROCHECK 62
4.5.3 Verify3D 65
4.5.4 ProSA-web 68
4.6 Structural Alignment between Wild-type NS1 Protein and
Mutants 71
4.7 Protein Side Chain Interactions 74
4.8 Prediction of Hot Spot Mutations 76
4.9 RNA Modeling and Validation 80
4.10 Molecular Docking Analysis 87
5 CONCLUSIONS AND FUTURE WORK
5.1 Conclusion 95
5.2 Future Works 96
REFERENCES 97
APPENDICES
APPENDIX A 111
xi
LIST OF TABLES
TABLE NO. TITLE PAGE
2.1 A brief summary on influenza A viral proteins and functions
(reviewed by O’Donnell and Subbarao, 2011) 8
2.2 NS1 protein amino acid functions. 15
4.1 NS1 variant library with change in chemical properties 56
4.2 Total energy of wild-type NS1A and mutant protein models 59
4.3 Validation of models using PROCHECK 64
4.4 RMSD calculations of mutant proteins 73
4.5 Mutability of wt NS1A protein residues obtained from error-prone
PCR 79
4.6 Secondary and tertiary of RNA aptamers predicted from
sequence 82
4.7 Validation of RNA aptamers via Molprobity 86
4.8 Docking energy or free energy of binding (kJ/mol) 87
4.9 List of hydrogen bonds between proteins and aptamers 88
4.10 Protein-RNA aptamer docking based on lowest free energy
conformation 93
xii
LIST OF FIGURES
FIGURE NO. TITLE PAGE
2.1 Structure of influenza A virus with 8 RNA segments that code
for viral proteins (Vincent et al., 2008) 7
2.2 Evolutional history of 2009 A (H1N1) virus (Khanna et al., 2009) 12
2.3 Diagram of NS1 protein structure and interactions with other
biological molecules (Hale et al., 2008) 14
2.4 Schematic diagram of error-prone PCR (Fujii et al., 2004) 21
2.5 Schematic diagram of steps involved for comparative protein
modeling (Sanchez et al., 2000) 24
2.6 Relationship between level of sequence identity in comparative
modeling and various applications in computational biology
(Sanchez et al., 2000) 25
2.7 Schematic diagram of SELEX process (Lee et al., 2010) 28
3.1 Map of yT&A cloning vector (Yeastern Biotech) 35
3.2 Multiple cloning sites in sequence of yT&A cloning
vector (Yeastern Biotech) 36
4.1 Effects of varying concentrations of MgCl2 on PCR products 42
4.2 PCR products with addition of MnCl2 ranging from 1µM to
20µM 43
xiii
4.3 PCR products with addition of MnCl2 ranging from 10 µM to
40 µM 44
4.4 PCR products with addition of MnCl2 ranging from 60 µM to
150 µM 44
4.5 DNA bands after error prone PCR of 80 cycles 45
4.6 Blue-white colonies on LB agar containing X-gal and IPTG after
TA cloning and transformation into E. coli DH5α 47
4.7 Screening of transformed colonies via colony PCR and products
resolved using gel electrophoresis 48
4.8 Screening of transformed colonies via colony PCR and products
resolved using gel electrophoresis 48
4.9 Screening of transformed colonies via colony PCR and products
resolved using gel electrophoresis 49
4.10 Screening of transformed colonies via colony PCR and products
resolved using gel electrophoresis 49
4.11 Screening of transformed colonies via colony PCR and products
resolved using gel electrophoresis 50
4.12 Nucleotide sequence of NS1A mutants aligned with the wild-type
NS1A gene for sequence comparison and identification of mutation
sites using Jalview program 51
4.13 Amino acid sequence of the mutant NS1A proteins aligned with the
amino acid sequence of NS1A protein for mutation identification
using Jalview program 54
4.14 Cartoon representation wild-type NS1 protein model
from influenza A virus (A/California/04/2009(H1N1)) viewed in
PyMOL 58
4.15 ERRAT plot of each protein with overall quality factor 61
xiv
4.16 Ramachandran plots generated via PROCHECK for different
protein structures 63
4.17 3D profile window plots of structures 66
4.18 Protein quality scores generated through ProSA web server 69
4.19 Structural alignment of all mutants against wt-NS1A protein
based on all Cα atoms with arrows pointing to mutation sites 72
4.20 Difference between wt NS1A and mutant proteins based on amino
acid side chain hydrogen bond interactions 74
4.21 The amino acid sequence of the wt NS1A protein with each
residue represented by mutability colour scale with 1 (lowest)
represented in blue to 9 (highest) represented in red 77
4.22 The ‘hot spots’ of wt-NS1A protein predicted via Hotspot Wizard
server prepared in PyMOL. The spheres in magenta indicate
‘hot spot’ residues. 78
4.23 Docking of wt-NS1A protein to aptamer 2 90
xv
LIST OF SYMBOLS/ ABBREVIATIONS/ NOTATIONS/ TERMINALOGY
A - Adenine
Ampr - Ampicillin resistant
BLAST - Basic Local Alignment Search Tool
bp - Base pairs
C - Cytosine
CASP - Critical Assessment of Structure Prediction
CPSF30 - 30-kDa subunit of the cellular cleavage and polyadenylation
specificity factor
dH2O - Distilled water
DNA - Deoxyribonucleic acid
dNTPs - Deoxynucleotide triphosphates
dsRNA - Double stranded RNA
E. coli - Escherichia coli
ED - Effector domain
eIF4F - Translation initiation factor
ELISA - Enzyme-linked immunosorbent assay
EP-PCR - Error-prone polymerase chain reaction
EtBr - Ethidium bromide
g - Gram
G - Gravitational force
G - Guanine
G-factor - Goodness factor
GUI - Graphical User Interface
h - Hour
HA - Hemagglutinin
H - Histidine
xvi
IFN - Interferon
IPTG - Isopropyl-β-D-thiogalactoside
K - Kelvin
Kd - Dissociation constant
kDa - Kilo Dalton
kJ - Kilo Joule
L - Liter
LB - Luria-Bertani
m - Mille
MFE - Minimum free energy
ml - Milliliter
mg/ml - Milligram/milliliter
Mg2+ - Magnesium ion
Mn2+ - Manganese ion
MgCl2 - Magnesium chloride
MnCl2 - Manganese chloride
mmol/L; mM - Milli molar
mRNA - Messenger RNA
NA - Neuraminidase
NaCl - Sodium chloride
NCBI - National Center for Biotechnology Information
NEP - Nuclear export protein
NES - Nuclear export signal
NLS - Nuclear localization sequence/signal
NoLS - Nucleolar localization signal
NMR - Nuclear magnetic resonance
ns - Nano second
No. - Number
NS1 - Nonstructural protein 1
OAS - Oligo (A) synthetase
PABP - Poly (A)-binding protein
PCR - Polymerase chain reaction
PDB - Protein Data Bank
PI3K - Phosphatidylinositol 3-kinase
xvii
PKR - Protein kinase R
ProSA - Protein Structure Analysis
ps - Pico second
RBD - dsRNA-binding domain
RMSD - Root mean square deviation
RNA - Ribonucleic acids
RNP - Ribonucleoprotein
rpm - Rounds per minute
s - Seconds
SDS-PAGE - Sodium dodecyl sulfate-polyacrylamide gel electrophoresis
SELEX - Systematic evolution of ligands by exponential enrichment