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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 BioinformaticsSchool of Biotechnology & Biological Sciences
West Bengal University of Technology Kolkata, India
International Conference on Bioinformatics (InCoB2009), September 7- 11, 2009
Singapore
It is thus an interaction of two proteins
one from plant
PolyGalacturonase-Inhibiting Protein (PGIP) is the protein of plant origin and is believed to have involvement in plant defence.
an enzyme from the fungus infecting the plant
PolyGalacturonase (PG) is the enzyme from the fungus.
another
PolyGalacturonase-Inhibiting Protein (PGIP) are believed to be proteins involved in plant defence
PGIP – the plant protein
Phaseolus vulgaris (bean)
Glycine max (soya bean)
Fusarium moniliforme is responsible for root rot, stem rot, foot rot, wilting etc
Pineapple –fusariose disease Fig- endosepsis
PG –the fungal enzyme
Fungicides- Chlorothalonil, mancozeb, drenches of thiophanate methyl
Fusarium moniliforme
Infected corn
Cell wall degradingCell wall degrading
Polygalacturonase(PGPolygalacturonase(PG))
Elicitor-activeElicitor-active
oligogalacturonoidesoligogalacturonoides
(OGAs) (OGAs)
Inactive
fragmentsC source
receptor
signal
cascade
Defense-related genes
Defense Defense
responseresponse
Cell Wall
Plasma
membrane
PGPG
HH
GG
AAPolygalacturonase Inhibiting ProteinPolygalacturonase Inhibiting Protein
(PGIP)(PGIP)
Fungal Fungal
pathogenpathogen
Model depicting the role
of PGIP-PG in plant
defence response
Nucleus
P
e
c
t
i
n
Interplay of PGIP and PG
PvPGIP1
PvPGIP2
GmPGIP3
FmPG
FmPG
does not
inhibit98%
inhibit
Bean
plant
Soya bean
plant
Fusarium
moniliforme
Recognition Specificity
88%
LRRNT_2 R1 R2 R3 R4 R5 R6 R7 R8 R9
60 152 178 224 271 291
297
311
LRRNT_2 R1 R2 R3 R4 R5 R6 R7 R8 R9
LRRNT_2 R5 R6 R7 R8 R9
311
297
290273
279266
232
227219
220192
160
145
136 143
116 140
10492
9590
84-88
82
72
70
67
59
54
42
29
R4R2 R3R1
PS PS PS PS
PvPGIP1
PvPGIP2
GmPGIP3
PS PS PS PS
PS PS PS PS
Domain architecture (DA) of the three PGIP molecules
Multiple sequence alignments of the
nine repeats of the PGIP
molecules
Ribbon representation of Crystal structure of PvPGIP2 (1OGQ)
PvPGIP2 PvPGIP1 GmPGIP3
Structure Already Solved
Structure not yet solved
Structure not yet solved
Structure Already Solved
FmPG
FmPG PvPGIP2 FmPG PvPGIP1 FmPG GmPGIP3
Docking
Energy minimization followed by Molecular Dynamics Simulation
GROMACS
GRAMM-X
MODELLER
Homology modeled
Homology modeled
PvPGIP1
GmPGIP3
Homology Models
Docked complexes of PGIP and FmPG
A. PvPGIP2 hinders the substrate binding site and blocks the active site cleft of FmPG
C. GmPGIP3 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
Electrostatic surface potential
PvPGIP1 PvPGIP2
GmPGIP3 FmPG
Electrostatic surface potential of the
three complexes
PvPGIP1-FmPG PvPGIP2-FmPG
GmPGIP3-FmPG
Active site residues 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
Change in Solvent Accessible Surface Area in FmPG
Interacting residues as found through mutational studies
with PvPGIP2
Change in SASA
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
Change in Solvent Accessible Surface Area in PGIPs
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
Electrostatic surface potential of PvPGIP2 with
a single mutation at 224
2.47Å
5.36Å
Wild type docked complex(PvPGIP2-FmPG)
Q224K
Q224
K300
K300
N C
C
C
Q224K mutant of the docked complex
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
Acknowledgment
Hiren GhoshAditi Maulik
Thank you!