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In silico modelling and molecular interaction of elongation factor receptor with pathogenic elongation factor tu 18

Plants depend entirely on innate immunity system to protect them from various pathogenic bacteria, fungi, and viruses. The first layer defense mechanism is named as Pattern-triggered immunity (PTI) system. It is activated by Pathogenassociated molecular pattern (PAMP) of the host plant by Pattern re...

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Main Author: Gunasekaran, Shivaranjini
Format: Thesis
Language:English
Published: 2019
Subjects:
Q Science (General)
Online Access:http://eprints.utm.my/id/eprint/102066/1/ShivaranjiGunasekaranMFS2019.pdf
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spelling my.utm.1020662023-07-31T07:42:02Z http://eprints.utm.my/id/eprint/102066/ In silico modelling and molecular interaction of elongation factor receptor with pathogenic elongation factor tu 18 Gunasekaran, Shivaranjini Q Science (General) Plants depend entirely on innate immunity system to protect them from various pathogenic bacteria, fungi, and viruses. The first layer defense mechanism is named as Pattern-triggered immunity (PTI) system. It is activated by Pathogenassociated molecular pattern (PAMP) of the host plant by Pattern recognition receptor (PRR) with the aid of co-receptor. Elongation factor receptor (EFR), which is also known as PRR, is one of the most recognized receptor used to protect against disease in Brassica species. Although research on transgenic approach and wet labs experiments have been carried out to analyse the EFR model, but the full ectodomain interactions of EFR with PAMP elf18 protein and co-receptor Brassinosteroid Insensitive 1-associated receptor kinases (BAK1) protein through in silico has not been accomplished yet. The purpose of this study was to determine the interaction of EFR protein with elf18 protein through in silico analysis approach. In this study, PRR EFR protein and PAMP elf18 protein was constructed by homology modelling using HHpred Modeller, followed by docking and molecular dynamics (MD) simulation of EFR protein and elf18 protein with co-receptor BAK1 protein (PDB:3UIM) and apo BAK1 (PDB ID:3ULZ) as model for mutant protein using ZDOCK 3.0.2 server and GROMACS 5.0.4 respectively. Finally, superimposition was done between EFR-elf18-BAK1 complex with existed FLS2-flg22-BAK1 crystal structure. Modelling results showed that multiple template modelling (MTM) generated best models compared to single template modelling (STM) due to their best quality of the protein structure obtained by HHpred Modeller generate best validation results of 71.123 ERRAT, 95.67% Verify3D and 92.8% in favoured region of Ramachandran Plot. Docking results showed that the complex interaction of BAK1 protein and elf18 protein binds at the concave surface of Leucine-Rich- Repeat (LRR) EFR, compatible with the existed FLS2 complex binding interactions. For the EFR-elf18-BAK1 (normal) complex, about 20 hydrogen bonds were sustained which is higher compared to EFR-elf18-BAK1 (mutated) complex that only sustained 16 hydrogen bonds, proved that the mutated protein have less interaction after simulation. After 50ns MD Simulation, the results showed that all the docked complexes has significant reduction of H-bonds. For EFR-elf18-BAK1 docked complex, H-bond between EFR protein and BAK1 protein reduced from 45 to 22, and H-bond between elf18 protein and BAK1 protein were reduced from 9 to 0 which caused by the conformational changes of the proteins during simulation. This study helps to understand the Brassica disease in detail and contribute significantly to early event of Pattern Triggered Immunity mechanism of EFR-elf18-BAK1 protein complex. 2019 Thesis NonPeerReviewed application/pdf en http://eprints.utm.my/id/eprint/102066/1/ShivaranjiGunasekaranMFS2019.pdf Gunasekaran, Shivaranjini (2019) In silico modelling and molecular interaction of elongation factor receptor with pathogenic elongation factor tu 18. Masters thesis, Universiti Teknologi Malaysia. http://dms.library.utm.my:8080/vital/access/manager/Repository/vital:146252
institution Universiti Teknologi Malaysia
building UTM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Teknologi Malaysia
content_source UTM Institutional Repository
url_provider http://eprints.utm.my/
language English
topic Q Science (General)
spellingShingle Q Science (General)
Gunasekaran, Shivaranjini
In silico modelling and molecular interaction of elongation factor receptor with pathogenic elongation factor tu 18
description Plants depend entirely on innate immunity system to protect them from various pathogenic bacteria, fungi, and viruses. The first layer defense mechanism is named as Pattern-triggered immunity (PTI) system. It is activated by Pathogenassociated molecular pattern (PAMP) of the host plant by Pattern recognition receptor (PRR) with the aid of co-receptor. Elongation factor receptor (EFR), which is also known as PRR, is one of the most recognized receptor used to protect against disease in Brassica species. Although research on transgenic approach and wet labs experiments have been carried out to analyse the EFR model, but the full ectodomain interactions of EFR with PAMP elf18 protein and co-receptor Brassinosteroid Insensitive 1-associated receptor kinases (BAK1) protein through in silico has not been accomplished yet. The purpose of this study was to determine the interaction of EFR protein with elf18 protein through in silico analysis approach. In this study, PRR EFR protein and PAMP elf18 protein was constructed by homology modelling using HHpred Modeller, followed by docking and molecular dynamics (MD) simulation of EFR protein and elf18 protein with co-receptor BAK1 protein (PDB:3UIM) and apo BAK1 (PDB ID:3ULZ) as model for mutant protein using ZDOCK 3.0.2 server and GROMACS 5.0.4 respectively. Finally, superimposition was done between EFR-elf18-BAK1 complex with existed FLS2-flg22-BAK1 crystal structure. Modelling results showed that multiple template modelling (MTM) generated best models compared to single template modelling (STM) due to their best quality of the protein structure obtained by HHpred Modeller generate best validation results of 71.123 ERRAT, 95.67% Verify3D and 92.8% in favoured region of Ramachandran Plot. Docking results showed that the complex interaction of BAK1 protein and elf18 protein binds at the concave surface of Leucine-Rich- Repeat (LRR) EFR, compatible with the existed FLS2 complex binding interactions. For the EFR-elf18-BAK1 (normal) complex, about 20 hydrogen bonds were sustained which is higher compared to EFR-elf18-BAK1 (mutated) complex that only sustained 16 hydrogen bonds, proved that the mutated protein have less interaction after simulation. After 50ns MD Simulation, the results showed that all the docked complexes has significant reduction of H-bonds. For EFR-elf18-BAK1 docked complex, H-bond between EFR protein and BAK1 protein reduced from 45 to 22, and H-bond between elf18 protein and BAK1 protein were reduced from 9 to 0 which caused by the conformational changes of the proteins during simulation. This study helps to understand the Brassica disease in detail and contribute significantly to early event of Pattern Triggered Immunity mechanism of EFR-elf18-BAK1 protein complex.
format Thesis
author Gunasekaran, Shivaranjini
author_facet Gunasekaran, Shivaranjini
author_sort Gunasekaran, Shivaranjini
title In silico modelling and molecular interaction of elongation factor receptor with pathogenic elongation factor tu 18
title_short In silico modelling and molecular interaction of elongation factor receptor with pathogenic elongation factor tu 18
title_full In silico modelling and molecular interaction of elongation factor receptor with pathogenic elongation factor tu 18
title_fullStr In silico modelling and molecular interaction of elongation factor receptor with pathogenic elongation factor tu 18
title_full_unstemmed In silico modelling and molecular interaction of elongation factor receptor with pathogenic elongation factor tu 18
title_sort in silico modelling and molecular interaction of elongation factor receptor with pathogenic elongation factor tu 18
publishDate 2019
url http://eprints.utm.my/id/eprint/102066/1/ShivaranjiGunasekaranMFS2019.pdf
http://eprints.utm.my/id/eprint/102066/
http://dms.library.utm.my:8080/vital/access/manager/Repository/vital:146252
_version_ 1773543499756470272
score 13.211869

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