“Modeling of binding interaction ofSystemin with its putative receptor

SR160”

Supervisor:-Mr Sumit GovilAssistant professorJaipur National University

Presented by:-Mohan KumarM.Sc BioinformaticsJaipur National University

University of Calcutta, Kolkata, under the guidance of Dr. Ansuman Lahiri

IntroductionProtein-protein interactions have very important roles at almost every level of cell function.

About 40% of all p-p interactions are protein with flexible peptides (Li et al., 2014).

Intrinsically disordered protein (IDPs) lack seconday and tertiary stable structure (Raveh et al., 2011).

The disordered segments of the peptides allow to interact with several proteins in multiple pathways hence associated with many disease(Babu MM. et al., 2011).

IDPs have important role in biological pathways in cell signaling, regulation, control and the functions of the living cell in plants.

Systemin:A Polypeptide Signal for Plant Defensive Genes

Systemin is a IDPs, found in tomato leaves contains 18 amino acids “AVQS KPPSKRDPPKMQTD”.

Firstly it was isolated from the leaves of Solanum lycopersicum in 1991.

Associated with the signal transduction pathway in the activation of systemic wound response.

Fig.1 showing the signaling pathway of Systemin.

Ryan and Pearce et al., 1998.

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 membrane bound 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 Showing systemin binding with its receptor 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 and unique island domain.

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

Steps

Model SR160 using Modeller.

Find binding site using PepsiteFinder and PatchDock.

Refinement of the final complex using FlexPepDock.

Prediction of final probable pose of complex using clustering.

3D structure prediction of SR160

SR160 3d structure Modelled using modeller9.14

Modelled structure validated using Vadar and Prosa web server.

Fig.4 Modelled structure of SR160.

Prediction of binding sites

Fig. 5 binding site predicted using Pepsite Finder tool.

Fig. 6 Binding site predicted using PatchDock tool.

Best ranked poses at probable binding sites

Fig. 7 showing the highest propensity for binding region.

Fig. 8 The best poses selected as probable complex of Systemin and SR160.

SUMMARY l 3D structure of the SR160 using

homology modelling.l Insilico approach used to study the

binding of systemin with its receptor.l Binding site prediction using blind

docking approach through Pepsitefinder and PatchDock.

l The reliable complex obtained was refined by the FlexPep-Dock server.

l selected the best poses.l Atomistic level of simulations can be

done for better prediction and insilico drug design.

Fig. 9 Final complex obtained.