Homology modelling and molecular dynamics study of plant defensin DM-AMP1


Abstract

Defensin in plants are the most important types of antimicrobial protein that provides the natural immunity against the pathogens. In the present work a stable protein model of plant Defensin DM-AMP1 has been proposed, whose three dimensional structure is not known. The method comprises the homology based modelling of the protein by using MODELLER program and validation of the model by various tools. Molecular dynamics simulation of the model protein was performed in water. The stability of the model was realised by computing root mean square deviation (RMSD) fluctuation of Carbon alpha back bone and potential energy value.



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