In-silico structural modeling and molecular dynamics simulation of pathogen-associated molecular pattern RaxX21

Abstract

The first layer of defence mechanism in plant known as pattern-triggered immunity (PTI) begins with the sense of pathogen-associated molecular patterns (PAMPs) by pattern-recognition receptors (PRRs). During the event PRRs bind with PAMPs and recruit co-receptor protein to activate the defence signal. To understand the mechanism properly, modeling of 3D structure of PAMPs and analysis of its structure is of huge importance. Although several plant PRRs have been discovered, but very few PAMPs have been discovered and characterized. This study describes the computational 3D modeling approach of a PAMP protein, RaxX21 and its important atomic characteristics. 3D structure shows that RaxX21 is mainly composed of coil structure. Also 500 ns MD simulation study reveals that sulfation at its tyrosine region which is done by the bacteria itself before secretion, remarkably improves the stability of RaxX21 which may contribute significantly in case of PTI.