Molecular dynamics simulations of the interactions between plant antimicrobial peptides and lipid membranes

Knottin-type peptides constitute the largest superfamily of gene-encoded plant antimicrobial peptides, which can act as molecular weapons to protect hosts from pathogen attacks. They exist either in a cyclic form as cyclotides or in a linear form as acyclotides. This study is focused on cyclotides,...

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Main Author: Lim, Melvin Wei Sheng
Other Authors: Lu Lanyuan
Format: Final Year Project
Language:English
Published: 2017
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Online Access:http://hdl.handle.net/10356/70784
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Institution: Nanyang Technological University
Language: English
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spelling sg-ntu-dr.10356-707842023-02-28T18:01:52Z Molecular dynamics simulations of the interactions between plant antimicrobial peptides and lipid membranes Lim, Melvin Wei Sheng Lu Lanyuan School of Biological Sciences DRNTU::Science::Biological sciences::Biophysics Knottin-type peptides constitute the largest superfamily of gene-encoded plant antimicrobial peptides, which can act as molecular weapons to protect hosts from pathogen attacks. They exist either in a cyclic form as cyclotides or in a linear form as acyclotides. This study is focused on cyclotides, which are further sub-classified into Möbius and bracelet cyclotides. They share a signature core comprising a cyclic cystine knot formed by six cysteine residues, and this often gives the presumption that the same loops in all cyclotides are responsible for interactions with membranes. However, findings from an NMR spectroscopy experiment showed that different binding modes are adopted for Möbius and bracelet cyclotides. Therefore, this study employed molecular dynamics simulations to compare the different ways by which the two families of cyclotides interact with membrane-mimicking micelles. Consequently, analysis of the interaction interface has shown that loops 1, 2, 5, and 6 of kB2 were identified at the peptide-micelle interface, whereas loops 2 and 3 of cO2 were consistently in contact with the micelle surface. In addition, these simulations have discovered two configurational states for kB2, which were previously not demonstrated. More importantly, this study confirms that hydrophobic interactions largely govern cyclotide-membrane interactions. Bachelor of Science in Biological Sciences 2017-05-11T05:47:52Z 2017-05-11T05:47:52Z 2017 Final Year Project (FYP) http://hdl.handle.net/10356/70784 en Nanyang Technological University 37 p. application/pdf
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic DRNTU::Science::Biological sciences::Biophysics
spellingShingle DRNTU::Science::Biological sciences::Biophysics
Lim, Melvin Wei Sheng
Molecular dynamics simulations of the interactions between plant antimicrobial peptides and lipid membranes
description Knottin-type peptides constitute the largest superfamily of gene-encoded plant antimicrobial peptides, which can act as molecular weapons to protect hosts from pathogen attacks. They exist either in a cyclic form as cyclotides or in a linear form as acyclotides. This study is focused on cyclotides, which are further sub-classified into Möbius and bracelet cyclotides. They share a signature core comprising a cyclic cystine knot formed by six cysteine residues, and this often gives the presumption that the same loops in all cyclotides are responsible for interactions with membranes. However, findings from an NMR spectroscopy experiment showed that different binding modes are adopted for Möbius and bracelet cyclotides. Therefore, this study employed molecular dynamics simulations to compare the different ways by which the two families of cyclotides interact with membrane-mimicking micelles. Consequently, analysis of the interaction interface has shown that loops 1, 2, 5, and 6 of kB2 were identified at the peptide-micelle interface, whereas loops 2 and 3 of cO2 were consistently in contact with the micelle surface. In addition, these simulations have discovered two configurational states for kB2, which were previously not demonstrated. More importantly, this study confirms that hydrophobic interactions largely govern cyclotide-membrane interactions.
author2 Lu Lanyuan
author_facet Lu Lanyuan
Lim, Melvin Wei Sheng
format Final Year Project
author Lim, Melvin Wei Sheng
author_sort Lim, Melvin Wei Sheng
title Molecular dynamics simulations of the interactions between plant antimicrobial peptides and lipid membranes
title_short Molecular dynamics simulations of the interactions between plant antimicrobial peptides and lipid membranes
title_full Molecular dynamics simulations of the interactions between plant antimicrobial peptides and lipid membranes
title_fullStr Molecular dynamics simulations of the interactions between plant antimicrobial peptides and lipid membranes
title_full_unstemmed Molecular dynamics simulations of the interactions between plant antimicrobial peptides and lipid membranes
title_sort molecular dynamics simulations of the interactions between plant antimicrobial peptides and lipid membranes
publishDate 2017
url http://hdl.handle.net/10356/70784
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