Insights from molecular modeling and dynamics simulation of pathogen resistance (R) protein from brinjal  


Dipty Shrivastava1, Vikrant Nain2, Shakti Sahi2, Anju Verma3, Priyanka Sharma1, Prakash Chand Sharma4, Polumetla Ananda Kumar1*


1National Research Centre on Plant Biotechnology, IARI, New Delhi -110012, India; 2School of Biotechnology, Gautam Buddha University, Greater Noida- 201308, India; 3School of Biological Sciences, University of Missouri, Kansas City MO- 64110, USA; 4School of Biotechnology, GGS Indraprastha University, Delhi-110403, India 


Article Type




Received November 24, 2010; Accepted December 18, 2010; Published January 22, 2011


Resistance (R) protein recognizes molecular signature of pathogen infection and activates downstream hypersensitive response signalling in plants. R protein works as a molecular switch for pathogen defence signalling and represent one of the largest plant gene family. Hence, understanding molecular structure and function of R proteins has been of paramount importance for plant biologists. The present study is aimed at predicting structure of R proteins signalling domains (CC-NBS) by creating a homology model, refining and optimising the model by molecular dynamics simulation and comparing ADP and ATP binding. Based on sequence similarity with proteins of known structures, CC-NBS domains were initially modelled using CED-4 (cell death abnormality protein) and APAF-1 (apoptotic protease activating factor) as multiple templates. The final CC-NBS structural model was built and optimized by molecular dynamic simulation for 5 nanoseconds (ns). Docking of ADP and ATP at active site shows that both ligand bind specifically with same residues and with minor difference (1 Kcal/mol) in binding energy. Sharing of binding site by ADP and ATP and low difference in their binding site makes CC-NBS suitable for working as molecular switch. Furthermore, structural superimposition elucidate that CC-NBS and CARD (caspase recruitment domains) domain of CED-4 have low RMSD value of 0.9 A0. Availability of 3D structural model for both CC and NBS domains will help in getting deeper insight in these pathogen defence genes.  


Shrivastava et al. Bioinformation 5(8): 326-330 (2011)

Edited by

P Kangueane






Biomedical Informatics



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