Comparative study of protein-protein interaction observed in PolyGalacturonase-Inhibiting Proteins from P. vulgaris and G. max and PolyGalacturonase from Fusarium moniliforme Soumalee Basu Department of Bioinformatics School of Biotechnology

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Comparative study of protein-protein interaction
observed inPolyGalacturonase-Inhibiting Proteins
from P. vulgaris and G. max and
PolyGalacturonase from Fusarium moniliforme
Soumalee Basu Department of BioinformaticsScho
ol of Biotechnology Biological Sciences West
Bengal University of Technology Kolkata, India
International Conference on
Bioinformatics (InCoB2009), September 7- 11, 2009
Singapore
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It is thus an interaction of two proteins
an enzyme from the fungus infecting the
plant PolyGalacturonase (PG) is the enzyme from
the fungus.
another
one from plant PolyGalacturonase-Inhibiting
Protein (PGIP) is the protein of plant origin and
is believed to have involvement in plant defence.
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PGIP the plant protein
PolyGalacturonase-Inhibiting Protein (PGIP) are
believed to be proteins involved in plant defence
Glycine max (soya bean)
Phaseolus vulgaris (bean)
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PG the fungal enzyme
Fusarium moniliforme is responsible for root rot,
stem rot, foot rot, wilting etc Pineapple
fusariose disease Fig- endosepsis
Fusarium moniliforme
Infected corn
Fungicides- Chlorothalonil, mancozeb, drenches of
thiophanate methyl
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Interplay of PGIP and PG
Cell Wall
Model depicting the role of PGIP-PG in plant
defence response
Plasma membrane
receptor
signal cascade
Elicitor-active oligogalacturonoides
(OGAs)
Fungal pathogen
P e c t i n
Nucleus
PG
Inactive fragments
Defense-related genes
C source
Cell wall degrading Polygalacturonase(PG)?
H G A
Defense response
Polygalacturonase Inhibiting Protein (PGIP)?
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Recognition Specificity
FmPG
PvPGIP1
does not inhibit
98
Bean plant
PvPGIP2
inhibit
FmPG
88
Fusarium moniliforme
GmPGIP3
Soya bean plant
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Domain architecture (DA) of the three PGIP
molecules
PvPGIP1
60
152
178
224
271
291
311
LRRNT_2
R1
R3
R2
R4
R5
R6
R7
R8
R9
297
PS
PS
PS
PS
PvPGIP2
LRRNT_2
R1
R3
R2
R4
R5
R6
R7
R8
R9
PS
PS
PS
PS
GmPGIP3
311
290
273
232
220
192
145
116
140
95
90
82
70
59
42
LRRNT_2
R4
R2
R1
R5
R6
R7
R8
R9
R3
72
297
279
266
227
219
160
136
143
104
92
84-88
67
54
29
PS
PS
PS
PS
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Multiple sequence alignments of the nine repeats
of the PGIP molecules
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Ribbon representation of Crystal structure of
PvPGIP2 (1OGQ)
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FmPG
PvPGIP2
PvPGIP1
GmPGIP3
Structure not yet solved
Structure not yet solved
Structure Already Solved
Structure Already Solved
MODELLER
Homology modeled
Homology modeled
GROMACS
Energy minimization followed by Molecular
Dynamics Simulation
GRAMM-X
Docking
FmPG
FmPG
FmPG
PvPGIP2
PvPGIP1
GmPGIP3
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Homology Models
PvPGIP1
GmPGIP3
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Docked complexes of PGIP and FmPG
A. PvPGIP2 hinders the substrate binding site
and blocks the active site cleft of FmPG
B. The only model of PvPGIP1-FmPG complex where
PvPGIP1 docks near the active site of FmPG
although not blocking it
C. GmPGIP3 hinders the substrate binding site and
blocks the active site cleft of FmPG
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Electrostatic surface potential
PvPGIP1
PvPGIP2
GmPGIP3
FmPG
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Electrostatic surface potential of the three
complexes
PvPGIP2-FmPG
PvPGIP1-FmPG
GmPGIP3-FmPG
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Change in Solvent Accessible Surface Area in FmPG
Active site residues Change in SASA due to complex formation Change in SASA due to complex formation Change in SASA due to complex formation
PvPGIP1 PvPGIP2 GmPGIP3

D(167) No Yes Yes
D(188) No Yes Yes
D(189) No Yes Yes
R(243) No Yes Yes
K(245) No Yes Yes
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Change in Solvent Accessible Surface Area in PGIPs
Interacting residues as found through mutational studies with PvPGIP2 Change in SASA Change in SASA Change in SASA
Interacting residues as found through mutational studies with PvPGIP2 PvPGIP2 PvPGIP1 (residues are different) GmPGIP3
V(152) Yes No Yes
S(178) Yes No Yes
Q(224) Yes No Yes
H(271) Yes No Yes
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Studies on ionic interaction of the complexes
reveal the interaction to play important role in
the PvPGIP2-FmPG and GmPGIP3-FmPG complexes
only Q(224)K mutation that was found to be
responsible for 70 reduction in inhibition
properties was next studied for using in silico
mutation
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Electrostatic surface potential of PvPGIP2 with
a single mutation at 224
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Q224K mutant of the docked complex
2.47Å
N
C
K300
Q224K
Wild type docked complex (PvPGIP2-FmPG)
C
5.36Å
K300
C
Q224
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Conclusion
Model three-dimensional structure of PvPGIP1
and GmPGIP3 show an rmsd of 1.45Aº and 1.66Aº
respectively with the template Docking
techniques suggest the mode of binding of the
fungal enzyme FmPG by PGIP2 from Phaseolus
vulgaris to be similar to that of its homologue
PGIP3 from Glycine max. In each case of binding,
PGIPs hinder the substrate binding site and block
the active site cleft of FmPG PGIP1 from the
same plant Phaseolus vulgaris which is incapable
of inhibiting FmPG, binds to FmPG in an evidently
different mode Electrostatic and van der Waals
interactions may play a significant role in PGIPs
for proper recognition and discrimination of PGs
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Acknowledgment
Hiren Ghosh
Aditi Maulik
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Thank you!