In silico molecular interactions study of pattern recognition receptor XA26 and plant pathogen-associated molecular patterns

Plants are sessile organisms that rely entirely on innate immune system for defense against pathogenic microbes or pest. First line defense of plant is known as pattern-triggered immunity (PTI). PTI is activated by pathogen-associated molecular patterns (PAMPs) of the host plant by pattern-recogniti...

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Main Author:	Ahmad Danian, Amirah Fathin
Format:	Thesis
Language:	English
Published:	2018
Subjects:	TP Chemical technology
Online Access:	http://eprints.utm.my/id/eprint/80888/1/AmirahFathinAhmadMFS2018.pdf
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spelling	my-utm-ep.808882019-07-24T00:10:18Z In silico molecular interactions study of pattern recognition receptor XA26 and plant pathogen-associated molecular patterns 2018-10 Ahmad Danian, Amirah Fathin TP Chemical technology Plants are sessile organisms that rely entirely on innate immune system for defense against pathogenic microbes or pest. First line defense of plant is known as pattern-triggered immunity (PTI). PTI is activated by pathogen-associated molecular patterns (PAMPs) of the host plant by pattern-recognition receptor (PRR) with the recruitment of co-receptor protein. Xa26 which is also known as PRR is one of the resistance gene in rice plant that protect against bacterial leaf blight disease, one of the most threatening disease that affect the yield of rice production. Although a few studies have been conducted on PRR Xa26, the detailed component involved in the interaction mechanism has not been elucidated. The purpose of this study was to explore protein interactions between PRR Xa26 with several PAMPs namely flg22 and RaxX21-sY. In this study, these two PAMPs were docked with PRR Xa26 in the presence of different co-receptor which are BAK1, OsSerk2 (PDB:4Q3G) and its mutant (PDB:4Q3I). PRR Xa26 protein model was constructed by homology modelling using Modeller HHpred followed by docking and molecular dynamics (MD) simulation of PRR Xa26 with the PAMPs using Zdock and GROMACS respectively. The modelling of PRR Xa26 by Modeller HHpred produced the best result with Verify 3D of 99.68%, ERRAT of 65.854% and 90.2% amino acid in allowed region of Ramachandran plot. Docking result showed that complex interaction of PRR Xa26, PAMP RaxX21-sY with co-receptor OsSerk2 (normal) bind at the concave portion of Xa26 leucine-rich repeat (LRR) which match with the flagellin sensitive 2 (FLS2) mediated PTI, the only crystallized structure in PTI till date. This is the best docking complex as it maintains protein conformational structure and provides stable binding interaction without any loss of bond after the simulation. MD simulation results showed significant reduction of hydrogen bonds for all the docked complex structures. For the Xa26_RaxX21- sY_OsSerk2 (normal) protein complex, the hydrogen bonds were reduced from 768 to 760. Whilst in mutated protein complex the numbers of hydrogen bond were reduced from 767 to 0. This significant reduction resulted in conformational changes of protein complex thus triggered the formation of salt bridge between Arg152 with the nearby residue Glu174 that caused binding disruption among the protein. This study provides significant information on the interaction between PRR Xa26 and multiple PAMPs to find the right PAMP for PTI mechanism of PRR Xa26. 2018-10 Thesis http://eprints.utm.my/id/eprint/80888/ http://eprints.utm.my/id/eprint/80888/1/AmirahFathinAhmadMFS2018.pdf application/pdf en public http://dms.library.utm.my:8080/vital/access/manager/Repository/vital:124846 masters Universiti Teknologi Malaysia, Faculty of Science Faculty of Science
institution	Universiti Teknologi Malaysia
collection	UTM Institutional Repository
language	English
topic	TP Chemical technology
spellingShingle	TP Chemical technology Ahmad Danian, Amirah Fathin In silico molecular interactions study of pattern recognition receptor XA26 and plant pathogen-associated molecular patterns
description	Plants are sessile organisms that rely entirely on innate immune system for defense against pathogenic microbes or pest. First line defense of plant is known as pattern-triggered immunity (PTI). PTI is activated by pathogen-associated molecular patterns (PAMPs) of the host plant by pattern-recognition receptor (PRR) with the recruitment of co-receptor protein. Xa26 which is also known as PRR is one of the resistance gene in rice plant that protect against bacterial leaf blight disease, one of the most threatening disease that affect the yield of rice production. Although a few studies have been conducted on PRR Xa26, the detailed component involved in the interaction mechanism has not been elucidated. The purpose of this study was to explore protein interactions between PRR Xa26 with several PAMPs namely flg22 and RaxX21-sY. In this study, these two PAMPs were docked with PRR Xa26 in the presence of different co-receptor which are BAK1, OsSerk2 (PDB:4Q3G) and its mutant (PDB:4Q3I). PRR Xa26 protein model was constructed by homology modelling using Modeller HHpred followed by docking and molecular dynamics (MD) simulation of PRR Xa26 with the PAMPs using Zdock and GROMACS respectively. The modelling of PRR Xa26 by Modeller HHpred produced the best result with Verify 3D of 99.68%, ERRAT of 65.854% and 90.2% amino acid in allowed region of Ramachandran plot. Docking result showed that complex interaction of PRR Xa26, PAMP RaxX21-sY with co-receptor OsSerk2 (normal) bind at the concave portion of Xa26 leucine-rich repeat (LRR) which match with the flagellin sensitive 2 (FLS2) mediated PTI, the only crystallized structure in PTI till date. This is the best docking complex as it maintains protein conformational structure and provides stable binding interaction without any loss of bond after the simulation. MD simulation results showed significant reduction of hydrogen bonds for all the docked complex structures. For the Xa26_RaxX21- sY_OsSerk2 (normal) protein complex, the hydrogen bonds were reduced from 768 to 760. Whilst in mutated protein complex the numbers of hydrogen bond were reduced from 767 to 0. This significant reduction resulted in conformational changes of protein complex thus triggered the formation of salt bridge between Arg152 with the nearby residue Glu174 that caused binding disruption among the protein. This study provides significant information on the interaction between PRR Xa26 and multiple PAMPs to find the right PAMP for PTI mechanism of PRR Xa26.
format	Thesis
qualification_level	Master's degree
author	Ahmad Danian, Amirah Fathin
author_facet	Ahmad Danian, Amirah Fathin
author_sort	Ahmad Danian, Amirah Fathin
title	In silico molecular interactions study of pattern recognition receptor XA26 and plant pathogen-associated molecular patterns
title_short	In silico molecular interactions study of pattern recognition receptor XA26 and plant pathogen-associated molecular patterns
title_full	In silico molecular interactions study of pattern recognition receptor XA26 and plant pathogen-associated molecular patterns
title_fullStr	In silico molecular interactions study of pattern recognition receptor XA26 and plant pathogen-associated molecular patterns
title_full_unstemmed	In silico molecular interactions study of pattern recognition receptor XA26 and plant pathogen-associated molecular patterns
title_sort	in silico molecular interactions study of pattern recognition receptor xa26 and plant pathogen-associated molecular patterns
granting_institution	Universiti Teknologi Malaysia, Faculty of Science
granting_department	Faculty of Science
publishDate	2018
url	http://eprints.utm.my/id/eprint/80888/1/AmirahFathinAhmadMFS2018.pdf
_version_	1747818275225468928

In silico molecular interactions study of pattern recognition receptor XA26 and plant pathogen-associated molecular patterns

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