Prediction of avian Influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin

1
Prediction of avian Influenza A binding
preference to human receptor using conformational
analysis of receptor bound to hemagglutinin

• Wanwimon Mokmak, M.Sc.
• Biostatistics and Informatics Laboratory
• Genome Institute, BIOTEC, Thailand

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Introduction

Avian influenza H5N1
Chain A of H5 HA (A/Duck/Singapore/3/97 HA)
Host cell receptor
Hemagglutinin protein
Ha, Y., et al. Proc.Natl.Acad.Sci.USA 98
11181-11186
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Introduction
Avian Influenza A virus
Avian receptor
Human receptor
F -55 degree Tran conformation
F 55 degree Cis conformation
HA Mutation
potentially changing the receptor binding
preference
Mutated KAN-1 Mutated Sing-97
Viseshakul N et al.Virology 2004, 328, 169-76
Hemagglutinin Protein
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Objectives

• To predict the HA binding selectivity from
  different HA variants
• in receptor-based conformational analysis by
  measuring
• a single torsion angle (F) during molecular
  dynamic simulation

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Material Method
X-ray crystal structures 1JSO template for
Sing-97 and Kan1 variant 1RVZ
template for Puerto 34 variant

• Known HA variants
• Sing-97
• Puerto-34 (human flu virus)
• Sing-97 variant
• (Q222L, G224S, Q222L/G224S)
• Kan-1
• Double KAN-1 mutant (L129V/A134V)

host cell receptor
X-ray structure or 3D- homology models of HA
protein

• Prediction for HA mutants
• Single Kan-1 HA
• M226T, K189G, K218S and L109P
• Puerto-34 HA variants
• Q222L, G224L, Q222L/G224S

HA complex
Observed torsion angle of host cell receptor
MD simulation
Binding preference
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Results Discussion
Comparison of observed torsion angle from
binding simulation
cis
Human receptor
Puerto-34

• Puerto-34
• bind preferentially
• with human type

tran
Avian receptor
Sing-97

• Sing-97
• bound better to
• Avian gt human
• Q222L/G224L sing-97
• bind preferentially
• with human type

Sing-97 Q222L Sing-97 G224S Sing-97 Q222L/G224S
Sing-97
cis

tran

• Kan-1
• bind better to
• Avian gt human
• L129V/A134V Kan-1
• bind preferentially
• with human type

Kan-1
cis
Kan-1 L129V/A134V KAN-1

tran
Harvey R et al. J Virol 2004, 78502-507.
Auewarakul P. et al. J Virol 2007,
819950-9955.
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Results Discussion
MD predicted receptor type selectivity of HAs
compared with data from published experimental
assays
Order of binding selectivity to human receptor
for flu viruses Puerto-34 gt L129V/A134V Kan-1?
Q222L/G224S Sing-97 gt Sing-97 ? Kan-1
Tested HA variants Simulation in vitro
Puerto-34
Sing-97
Q222L Sing-97
G224S Sing-97
Q222L/G224S Sing-97
Kan-1
L129V/A134V Kan-1
most preferred, moderately preferred,
least preferred
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Results Discussion
Prediction of the Relative Binding Selectivity
Simulation results of four Kan-1 HA mutant
variants binding to Human receptor
Cis
Tran
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Results Discussion
Prediction of the Relative Binding Selectivity
Simulation results of four Puerto-34 HA mutants

Cis
Tran
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Conclusions
Binding Preference

• Human receptor associates with positive
  F angle
• (Cis conformation)
• Avian-type receptor associates with negative -F
  angle
• (Tran conformation)
• Using Molecular dynamics simulation to
  observe torsion
• angles

in silico Mutagenesis
Emerging Epidemics
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Acknowledgements
Dr. Sissades Tongsima Dr. Chak Sangma Ms.Nipa
Jongkon Ms.Daungmanee Chuakheaw Mr. Anunchai
Assawamakin Dr. Philip J. Shaw Dr. Jittima
Piriyapongsa
National Center for Genetic Engineering and
Biotechnology (BIOTEC) Kasetsart University
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THANK YOU
THANK YOU
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Material Method

• X-ray structure to prepare HA variant for MD
  simulation
• 1JSN 1JSO template for Sing-97 and Kan1
  variants
• 1RVX 1RVZ template for Puerto 34

HA variants and prediction HA variants used for
simulation

• HA variants
• Sing-97
• Mutated Singe-97
• (Q222L, G224S, Q222L/G224S)
• KAN-1
• mutated KAN-1 (L129V/A134V)
• Puerto-34
• available binding assay

• Prediction model
• Kan-1 HA variant
• M226T, K189G, K218S and L109P
• Puerto-34 HA variant
• Q222L, G224L, Q222L/G224S

• Using the SANDER module in the AMBER9 program

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Results Discussion
Six nanosecond RMSD plots of three simulation HA
system
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Materials and Methods

• Molecular dynamic simulations
• Glycam04 parameters for receptor
• AMBER 2003 force field for protein
• using the TIP5P water model in the truncated
  octahedron box
• Using the SANDER module in the AMBER9 program

To determine the binding preference
F angle approximately -55 degrees
F angle approximately 55 degrees
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Results Discussion
Results Discussion
Figure 3. Comparison of observed torsion angle
(F) from the binding simulation between HA
variants and avian and human type receptor
analog.
Puerto-34
Siaa(2,3)Gal
Siaa(2,6)Gal
F Was monitored and interpreted in term of the
binding preference
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Results Discussion
Comparison of observed torsion angle (F) from the
binding simulation between HA variants and avian
and human type receptor analog.
Sing-97
Siaa(2,3)Gal
Siaa(2,6)Gal
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Results Discussion
Figure 3. Comparison of observed torsion angle
(F) from the binding simulation between HA
variants and avian and human type receptor
analog.
Kan-1
Siaa(2,3)Gal
Siaa(2,6)Gal
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Results Discussion
Torsion angles of selected glycosides from PDB
PDB code HA Type Ligand Type Sugar Units Torsion (F) Resolution (Å)
1JSI A/Swine/Hong Kong/9/98H9 Siaa(2,6)Gal Sia-Gal-GlcNAc-Gal-Glc 56.2 2.4
1JSO A/Duck/Singapore/3/97H5 Siaa(2,6)Gal Sia - 2.4
1RVT A/Swine/Iowa/15/30H1 Siaa(2,6)Gal Sia-Gal-GlcNAc-Gal-Glc 69.7 2.4
1RVZ A/Puerto Rico/8/34H1 Siaa(2,6)Gal Sia-Gal-GlcNAc 67.6 2.25
1JSN A/Duck/Singapore/3/97H5 Siaa(2,3)Gal Sia-Gal-GlcNAc -55.1 2.4
1RVX A/Puerto Rico/8/34H1 Siaa(2,3)Gal Sia-Gal-GlcNAc -59.1 2.2