Modelling of binding interaction of

systemin with its putative receptor

SR160
Mohan Kumar
M.Sc Bioinformatics
JNU,Jaipur

Proteinprotein interactions have very important roles at almost

everylevelofcellfunction.
About40%ofallppinteractionsareproteinwithflexiblepeptides
(Lietal.,2014).
Intrinsically disordered protein (IDPs) lack seconday and tertiary
stablestructure(Ravehetal.,2011).
The disordered segments of the peptides allow to interact with
several proteins in multiple pathways hence associated with many
disease(BabuMM.etal.,2011).

IDPshaveimportantroleinbiologicalpathwaysincellsignalaning,
regulation,controlandthefunctionsofthelivingcellinplants.

SYSTEMIN: A Polypeptide Signal for Plant Defensive Genes

Systemin is a IDPs, found in

tomato leaves contains 18 amino
acids.
AVQSKPPSKRDPPKMQTD
Firstly it was isolated from the
leaves of Solanum lycopersicum
in1991.
Associated
with
the
signaltransductionpathwayinthe
activation of systemic wound
response.

RyanandPearceetal.,1998.

Fig.1 showing the signaling

pathway of Systemin.

Systemin receptor SR160

Systemin causes a cascade of

intracellular signaling events which
lead to the activation of defensive
genes.
The pathways are initiated by the
release of systemin at wound sites
and its interaction with a membranebound receptor from Scheer and Ryan
et al.,2002.
The identification of loss-of-function
mutants of tomato SR160 gene would
distinguish these two possibilities and
also would be important confirmation
that SR160 is the systemin receptor
from Yin et al., 2002.

Fig.2 from Ryan and Pearce et al.,

2003

SR160 simililar with BRI1

The predicted SR160 protein

shows the higher similarity with
BRI1.
Both contain 25 LRRs
unique island domain.

and

83% transmembrane and 90%

kinases domains of SR160
identical with BRI1.
SR160 and BRI1 do not have the
same binding site.
Fig.3 SR160 showing the
similarity with BRI1.

Yin et al., 2002

Following steps were involved:

Model SR160 using Modeller9.14.

Find binding site using PepsiteFinder and PatchDock.

Refinement of the final complex using FlexPepDock.

Understanding the dynamic binding using molecular dynamic simulation.

SR160 3d structure Modeled using modeller9.14

Searching the homologous sequence.

Selecting a template.

Aligning query sequence with selected template.

Model building.

Model evaluation.

Fig.5 Homologous sequences obtained from build_profile.py file.

Fig.6 showing the result of compare.log file.

>> Summary of successfully produced models:

Filename

molpdf

DOPE score

GA341 score

---------------------------------------------------------------------SR160.B99990001.pdb

5355.24414 -84000.07812

1.00000

SR160.B99990002.pdb

5433.86914 -82970.92969

1.00000

SR160.B99990003.pdb

5381.18994 -83419.46094

1.00000

SR160.B99990004.pdb

5429.87793 -84220.21094

1.00000

SR160.B99990005.pdb

5474.54053 -83519.13281

1.00000

Total CPU time [seconds]

343.71

Fig.7 shows the result summary obtained in model.log file.

Fig.8 graphshowingoverall

modelqualityusingZscore
usingProsaserver.

Fig. 9 graph showing local model

quality obtained using Prosa
server.

StatisticObservedExpected
Resolution
RValue
#resinphipsicore618(83%)666(90%)
#resinphipsiallowed116(15%)52(7%)
#resinphipsigenerous5(0%)7(1%)
#resinphipsioutside1(0%)0(0%)
#resinomegacore677(91%)710(96%)
#resinomegaallowed49(6%)22(3%)
#resinomegagenerous11(1%)0(0%)
#resinomegaoutside3(0%)7(1%)
#packingdefects15951
Freeenergyoffolding765.58716.58
#res95%buried224349
#buriedcharges80

Fig.10 Result obtained from VADAR online server.

The 3D structure of systemin

receptorSR160modeled.
ValidatedusingonlineVADAR
server and Prosa server
showed reliable structure for
furtherstudyandanalysis.

Fig.11 Modeled structure of SR160

using modeller9.14.

Binding site prediction using PepSiteFinder

Fig.12 showing the plowchart of

PepSiteFinder from Saladin et al., 2014.

Fig.13 result obtained from the

PepSiteFinder.

Find binding site using PatchDock

Fig.14 showing the steps in PatchDock from

http://bioinfo3d.cs.tau.ac.il/PatchDock/patchdock.html.

Fig.15 showing the complex poseses at probable binding sites obtained from PatchDock.

Fig.16 showing the selected pose from the PatchDock result.

Refinement of the complex using FlexPepDock

Fig.17 showing the steps in FlexPepDock from .

Result of FlexPepDock

Fig.26 Showing the graph between reweighted vs rmsAll.

Fig.27 Showing the graph between total score vs rmsAll

The best complex obtained

Fig.23 Showing best poses obtained through clustering.

Summary

We have used insilico approach to study the binding behaviour of the

systemin peptide with its putative receptor SR160.

We have predicted the 3D structure of the SR160 using homology modeling.

Binding site prediction using blind docking approach through Pepsitefinder

and validated with PatchDock.

The reliable complex obtained was refined by the FlexPep-Dock server and
selected the best poses.

For better analysis of binding interaction we can do atomistic level of

simulations that may help in better prediction and future insilico drug design.

Summary

We have used insilico approach to study the binding behaviour of the

systemin peptide with its putative receptor SR160.

We have predicted the 3D structure of the SR160 using homology modeling.

Binding site prediction using blind docking approach through Pepsitefinder

and validated with PatchDock.

The reliable complex obtained was refined by the FlexPep-Dock server and
selected the best poses.

For better analysis of binding interaction we can do atomistic level of

simulations that may help in better prediction and future insilico drug design.