Molecular dynamics modelling of EGCG clusters on ceramide bilayers

Jingjie Yeo; Yuan Cheng; Weifeng Li; Yong Wei Zhang

doi:10.1063/1.4938968

Molecular dynamics modelling of EGCG clusters on ceramide bilayers

Jingjie Yeo, Yuan Cheng, Weifeng Li, Yong Wei Zhang

Research output: Chapter in Book/Report/Conference proceeding › Conference Paper › Other

Abstract

A novel method of atomistic modelling and characterization of both pure ceramide and mixed lipid bilayers is being developed, using only the General Amber ForceField. Lipid bilayers modelled as pure ceramides adopt hexagonal packing after equilibration, and the area per lipid and bilayer thickness are consistent with previously reported theoretical results. Mixed lipid bilayers are modelled as a combination of ceramides, cholesterol, and free fatty acids. This model is shown to be stable after equilibration. Green tea extract, also known as epigallocatechin-3-gallate, is introduced as a spherical cluster on the surface of the mixed lipid bilayer. It is demonstrated that the cluster is able to bind to the bilayers as a cluster without diffusing into the surrounding water.

Original language	English
Title of host publication	International Conference of Computational Methods in Sciences and Engineering 2015, ICCMSE 2015
Editors	Zacharoula Kalogiratou, Theodore E. Simos, Theodore Monovasilis, Theodore E. Simos, Theodore E. Simos
Publisher	American Institute of Physics
ISBN (Electronic)	9780735413498
DOIs	https://doi.org/10.1063/1.4938968
Publication status	Published - 31 Dec 2015
Externally published	Yes
Event	International Conference of Computational Methods in Sciences and Engineering 2015 - Athens, Greece Duration: 20 Mar 2015 → 23 Mar 2015 https://aip.scitation.org/toc/apc/1702/1 (Proceedings)

Publication series

Name	AIP Conference Proceedings
Volume	1702
ISSN (Print)	0094-243X
ISSN (Electronic)	1551-7616

Conference

Conference	International Conference of Computational Methods in Sciences and Engineering 2015
Abbreviated title	ICCMSE 2015
Country/Territory	Greece
City	Athens
Period	20/03/15 → 23/03/15
Internet address	https://aip.scitation.org/toc/apc/1702/1 (Proceedings)

Keywords

Ceramides
EGCG
Lipid Bilayer
Molecular Dynamics

Access to Document

10.1063/1.4938968

Cite this

Yeo, J., Cheng, Y., Li, W., & Zhang, Y. W. (2015). Molecular dynamics modelling of EGCG clusters on ceramide bilayers. In Z. Kalogiratou, T. E. Simos, T. Monovasilis, T. E. Simos, & T. E. Simos (Eds.), International Conference of Computational Methods in Sciences and Engineering 2015, ICCMSE 2015 [190001] (AIP Conference Proceedings; Vol. 1702). American Institute of Physics. https://doi.org/10.1063/1.4938968

Yeo, Jingjie ; Cheng, Yuan ; Li, Weifeng et al. / Molecular dynamics modelling of EGCG clusters on ceramide bilayers. International Conference of Computational Methods in Sciences and Engineering 2015, ICCMSE 2015. editor / Zacharoula Kalogiratou ; Theodore E. Simos ; Theodore Monovasilis ; Theodore E. Simos ; Theodore E. Simos. American Institute of Physics, 2015. (AIP Conference Proceedings).

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title = "Molecular dynamics modelling of EGCG clusters on ceramide bilayers",

abstract = "A novel method of atomistic modelling and characterization of both pure ceramide and mixed lipid bilayers is being developed, using only the General Amber ForceField. Lipid bilayers modelled as pure ceramides adopt hexagonal packing after equilibration, and the area per lipid and bilayer thickness are consistent with previously reported theoretical results. Mixed lipid bilayers are modelled as a combination of ceramides, cholesterol, and free fatty acids. This model is shown to be stable after equilibration. Green tea extract, also known as epigallocatechin-3-gallate, is introduced as a spherical cluster on the surface of the mixed lipid bilayer. It is demonstrated that the cluster is able to bind to the bilayers as a cluster without diffusing into the surrounding water.",

keywords = "Ceramides, EGCG, Lipid Bilayer, Molecular Dynamics",

author = "Jingjie Yeo and Yuan Cheng and Weifeng Li and Zhang, {Yong Wei}",

note = "Publisher Copyright: {\textcopyright} 2015 AIP Publishing LLC.; International Conference of Computational Methods in Sciences and Engineering 2015, ICCMSE 2015 ; Conference date: 20-03-2015 Through 23-03-2015",

year = "2015",

month = dec,

day = "31",

doi = "10.1063/1.4938968",

language = "English",

series = "AIP Conference Proceedings",

publisher = "American Institute of Physics",

editor = "Zacharoula Kalogiratou and Simos, {Theodore E.} and Theodore Monovasilis and Simos, {Theodore E.} and Simos, {Theodore E.}",

booktitle = "International Conference of Computational Methods in Sciences and Engineering 2015, ICCMSE 2015",

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Yeo, J, Cheng, Y, Li, W & Zhang, YW 2015, Molecular dynamics modelling of EGCG clusters on ceramide bilayers. in Z Kalogiratou, TE Simos, T Monovasilis, TE Simos & TE Simos (eds), International Conference of Computational Methods in Sciences and Engineering 2015, ICCMSE 2015., 190001, AIP Conference Proceedings, vol. 1702, American Institute of Physics, International Conference of Computational Methods in Sciences and Engineering 2015, Athens, Greece, 20/03/15. https://doi.org/10.1063/1.4938968

Molecular dynamics modelling of EGCG clusters on ceramide bilayers. / Yeo, Jingjie; Cheng, Yuan; Li, Weifeng et al.

International Conference of Computational Methods in Sciences and Engineering 2015, ICCMSE 2015. ed. / Zacharoula Kalogiratou; Theodore E. Simos; Theodore Monovasilis; Theodore E. Simos; Theodore E. Simos. American Institute of Physics, 2015. 190001 (AIP Conference Proceedings; Vol. 1702).

Research output: Chapter in Book/Report/Conference proceeding › Conference Paper › Other

TY - GEN

T1 - Molecular dynamics modelling of EGCG clusters on ceramide bilayers

AU - Yeo, Jingjie

AU - Cheng, Yuan

AU - Li, Weifeng

AU - Zhang, Yong Wei

PY - 2015/12/31

Y1 - 2015/12/31

N2 - A novel method of atomistic modelling and characterization of both pure ceramide and mixed lipid bilayers is being developed, using only the General Amber ForceField. Lipid bilayers modelled as pure ceramides adopt hexagonal packing after equilibration, and the area per lipid and bilayer thickness are consistent with previously reported theoretical results. Mixed lipid bilayers are modelled as a combination of ceramides, cholesterol, and free fatty acids. This model is shown to be stable after equilibration. Green tea extract, also known as epigallocatechin-3-gallate, is introduced as a spherical cluster on the surface of the mixed lipid bilayer. It is demonstrated that the cluster is able to bind to the bilayers as a cluster without diffusing into the surrounding water.

AB - A novel method of atomistic modelling and characterization of both pure ceramide and mixed lipid bilayers is being developed, using only the General Amber ForceField. Lipid bilayers modelled as pure ceramides adopt hexagonal packing after equilibration, and the area per lipid and bilayer thickness are consistent with previously reported theoretical results. Mixed lipid bilayers are modelled as a combination of ceramides, cholesterol, and free fatty acids. This model is shown to be stable after equilibration. Green tea extract, also known as epigallocatechin-3-gallate, is introduced as a spherical cluster on the surface of the mixed lipid bilayer. It is demonstrated that the cluster is able to bind to the bilayers as a cluster without diffusing into the surrounding water.

KW - Ceramides

KW - EGCG

KW - Lipid Bilayer

KW - Molecular Dynamics

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U2 - 10.1063/1.4938968

DO - 10.1063/1.4938968

M3 - Conference Paper

AN - SCOPUS:84984583501

T3 - AIP Conference Proceedings

BT - International Conference of Computational Methods in Sciences and Engineering 2015, ICCMSE 2015

A2 - Kalogiratou, Zacharoula

A2 - Simos, Theodore E.

A2 - Monovasilis, Theodore

A2 - Simos, Theodore E.

PB - American Institute of Physics

T2 - International Conference of Computational Methods in Sciences and Engineering 2015

Y2 - 20 March 2015 through 23 March 2015

ER -

Yeo J, Cheng Y, Li W, Zhang YW. Molecular dynamics modelling of EGCG clusters on ceramide bilayers. In Kalogiratou Z, Simos TE, Monovasilis T, Simos TE, Simos TE, editors, International Conference of Computational Methods in Sciences and Engineering 2015, ICCMSE 2015. American Institute of Physics. 2015. 190001. (AIP Conference Proceedings). https://doi.org/10.1063/1.4938968

Molecular dynamics modelling of EGCG clusters on ceramide bilayers

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