Evaluation of the Binding Mechanism of Human Defensin 5 in a Bacterial Membrane: A Simulation Study

Human α-defensin 5 (HD5) is a host-defense peptide exhibiting broad-spectrum antimicrobial activity. The lipopolysaccharide (LPS) layer on the Gram-negative bacterial membrane acts as a barrier to HD5 insertion. Therefore, the pore formation and binding mechanism remain unclear. Here, the binding me...

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Autores principales:	Tadsanee Awang, Phoom Chairatana, Ranjit Vijayan, Prapasiri Pongprayoon
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	antimicrobial peptides human defensin 5 lipopolysaccharide molecular dynamics simulations Biology (General) QH301-705.5 Chemistry QD1-999
Acceso en línea:	https://doaj.org/article/177ae3a9ed9946e286467fdfb406fde5
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spelling	oai:doaj.org-article:177ae3a9ed9946e286467fdfb406fde52021-11-25T17:56:19ZEvaluation of the Binding Mechanism of Human Defensin 5 in a Bacterial Membrane: A Simulation Study10.3390/ijms2222124011422-00671661-6596https://doaj.org/article/177ae3a9ed9946e286467fdfb406fde52021-11-01T00:00:00Zhttps://www.mdpi.com/1422-0067/22/22/12401https://doaj.org/toc/1661-6596https://doaj.org/toc/1422-0067Human α-defensin 5 (HD5) is a host-defense peptide exhibiting broad-spectrum antimicrobial activity. The lipopolysaccharide (LPS) layer on the Gram-negative bacterial membrane acts as a barrier to HD5 insertion. Therefore, the pore formation and binding mechanism remain unclear. Here, the binding mechanisms at five positions along the bacterial membrane axis were investigated using Molecular Dynamics. (MD) simulations. We found that HD5 initially placed at positions 1 to 3 moved up to the surface, while HD5 positioned at 4 and 5 remained within the membrane interacting with the middle and inner leaflet of the membrane, respectively. The arginines were key components for tighter binding with 3-deoxy-d-manno-octulosonic acid (KDO), phosphates of the outer and inner leaflets. KDO appeared to retard the HD5 penetration.Tadsanee AwangPhoom ChairatanaRanjit VijayanPrapasiri PongprayoonMDPI AGarticleantimicrobial peptideshuman defensin 5lipopolysaccharidemolecular dynamics simulationsBiology (General)QH301-705.5ChemistryQD1-999ENInternational Journal of Molecular Sciences, Vol 22, Iss 12401, p 12401 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	antimicrobial peptides human defensin 5 lipopolysaccharide molecular dynamics simulations Biology (General) QH301-705.5 Chemistry QD1-999
spellingShingle	antimicrobial peptides human defensin 5 lipopolysaccharide molecular dynamics simulations Biology (General) QH301-705.5 Chemistry QD1-999 Tadsanee Awang Phoom Chairatana Ranjit Vijayan Prapasiri Pongprayoon Evaluation of the Binding Mechanism of Human Defensin 5 in a Bacterial Membrane: A Simulation Study
description	Human α-defensin 5 (HD5) is a host-defense peptide exhibiting broad-spectrum antimicrobial activity. The lipopolysaccharide (LPS) layer on the Gram-negative bacterial membrane acts as a barrier to HD5 insertion. Therefore, the pore formation and binding mechanism remain unclear. Here, the binding mechanisms at five positions along the bacterial membrane axis were investigated using Molecular Dynamics. (MD) simulations. We found that HD5 initially placed at positions 1 to 3 moved up to the surface, while HD5 positioned at 4 and 5 remained within the membrane interacting with the middle and inner leaflet of the membrane, respectively. The arginines were key components for tighter binding with 3-deoxy-d-manno-octulosonic acid (KDO), phosphates of the outer and inner leaflets. KDO appeared to retard the HD5 penetration.
format	article
author	Tadsanee Awang Phoom Chairatana Ranjit Vijayan Prapasiri Pongprayoon
author_facet	Tadsanee Awang Phoom Chairatana Ranjit Vijayan Prapasiri Pongprayoon
author_sort	Tadsanee Awang
title	Evaluation of the Binding Mechanism of Human Defensin 5 in a Bacterial Membrane: A Simulation Study
title_short	Evaluation of the Binding Mechanism of Human Defensin 5 in a Bacterial Membrane: A Simulation Study
title_full	Evaluation of the Binding Mechanism of Human Defensin 5 in a Bacterial Membrane: A Simulation Study
title_fullStr	Evaluation of the Binding Mechanism of Human Defensin 5 in a Bacterial Membrane: A Simulation Study
title_full_unstemmed	Evaluation of the Binding Mechanism of Human Defensin 5 in a Bacterial Membrane: A Simulation Study
title_sort	evaluation of the binding mechanism of human defensin 5 in a bacterial membrane: a simulation study
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/177ae3a9ed9946e286467fdfb406fde5
work_keys_str_mv	AT tadsaneeawang evaluationofthebindingmechanismofhumandefensin5inabacterialmembraneasimulationstudy AT phoomchairatana evaluationofthebindingmechanismofhumandefensin5inabacterialmembraneasimulationstudy AT ranjitvijayan evaluationofthebindingmechanismofhumandefensin5inabacterialmembraneasimulationstudy AT prapasiripongprayoon evaluationofthebindingmechanismofhumandefensin5inabacterialmembraneasimulationstudy
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Evaluation of the Binding Mechanism of Human Defensin 5 in a Bacterial Membrane: A Simulation Study

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