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CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides

CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides
CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides
A complex cell envelope, composed of a mixture of lipid types including lipopolysaccharides, protects bacteria from the external environment. Clearly, the proteins embedded within the various components of the cell envelope have an intricate relationship with their local environment. Therefore, to obtain meaningful results, molecular simulations need to mimic as far as possible this chemically heterogeneous system. However, setting up such systems for computational studies is far from trivial, and consequently the vast majority of simulations of outer membrane proteins still rely on oversimplified phospholipid membrane models. This work presents an update of CHARMM-GUI Martini Maker for coarse-grained modeling and simulation of complex bacterial membranes with lipopolysaccharides. The qualities of the outer membrane systems generated by Martini Maker are validated by simulating them in bilayer, vesicle, nanodisc, and micelle environments (with and without outer membrane proteins) using the Martini force field. We expect this new feature in Martini Maker to be a useful tool for modeling large, complicated bacterial outer membrane systems in a user-friendly manner.
1096-987X
2354-2363
Hsu, Pin-Chia
4b4c8c18-752e-4ba8-a456-0fc71df1b286
Bruininks, Bart M.H.
25a9457e-232d-4ea2-bcbf-68380284b7ea
Jefferies, Damien, Francis
8df97e21-8df6-4571-bfbe-3edc41e16967
Souza, Paulo C.T.
f3e51feb-f515-42ec-8acb-7f8570123b0c
Lee, Jumin
e7171f0b-bdbe-43c2-b8ef-b47b01c22417
Patel, Dhilon S.
7c0bb39e-ecec-405d-9f08-a39266ab2c3c
Marrink, Siewert J.
3981de06-1037-4ebd-8bd8-d6997d82815c
Qi, Yifei
5151661f-8b67-47c1-aecd-4ff929a1ff0e
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
Im, Wonpil
2eead34b-7a3e-4e01-ab2a-b3b7450e5f79
Hsu, Pin-Chia
4b4c8c18-752e-4ba8-a456-0fc71df1b286
Bruininks, Bart M.H.
25a9457e-232d-4ea2-bcbf-68380284b7ea
Jefferies, Damien, Francis
8df97e21-8df6-4571-bfbe-3edc41e16967
Souza, Paulo C.T.
f3e51feb-f515-42ec-8acb-7f8570123b0c
Lee, Jumin
e7171f0b-bdbe-43c2-b8ef-b47b01c22417
Patel, Dhilon S.
7c0bb39e-ecec-405d-9f08-a39266ab2c3c
Marrink, Siewert J.
3981de06-1037-4ebd-8bd8-d6997d82815c
Qi, Yifei
5151661f-8b67-47c1-aecd-4ff929a1ff0e
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
Im, Wonpil
2eead34b-7a3e-4e01-ab2a-b3b7450e5f79

Hsu, Pin-Chia, Bruininks, Bart M.H., Jefferies, Damien, Francis, Souza, Paulo C.T., Lee, Jumin, Patel, Dhilon S., Marrink, Siewert J., Qi, Yifei, Khalid, Syma and Im, Wonpil (2017) CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides. Journal of Computational Chemistry, 38 (27), 2354-2363. (doi:10.1002/jcc.24895).

Record type: Article

Abstract

A complex cell envelope, composed of a mixture of lipid types including lipopolysaccharides, protects bacteria from the external environment. Clearly, the proteins embedded within the various components of the cell envelope have an intricate relationship with their local environment. Therefore, to obtain meaningful results, molecular simulations need to mimic as far as possible this chemically heterogeneous system. However, setting up such systems for computational studies is far from trivial, and consequently the vast majority of simulations of outer membrane proteins still rely on oversimplified phospholipid membrane models. This work presents an update of CHARMM-GUI Martini Maker for coarse-grained modeling and simulation of complex bacterial membranes with lipopolysaccharides. The qualities of the outer membrane systems generated by Martini Maker are validated by simulating them in bilayer, vesicle, nanodisc, and micelle environments (with and without outer membrane proteins) using the Martini force field. We expect this new feature in Martini Maker to be a useful tool for modeling large, complicated bacterial outer membrane systems in a user-friendly manner.

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LPS_Martini_Maker_main_final - Accepted Manuscript
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Accepted/In Press date: 9 July 2017
e-pub ahead of print date: 3 August 2017
Published date: 15 October 2017

Identifiers

Local EPrints ID: 413877
URI: http://eprints.soton.ac.uk/id/eprint/413877
ISSN: 1096-987X
PURE UUID: 6927c379-7428-4f97-8647-4f2dc128fb9e
ORCID for Syma Khalid: ORCID iD orcid.org/0000-0002-3694-5044

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Date deposited: 08 Sep 2017 16:30
Last modified: 07 Oct 2020 05:32

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Contributors

Author: Pin-Chia Hsu
Author: Bart M.H. Bruininks
Author: Damien, Francis Jefferies
Author: Paulo C.T. Souza
Author: Jumin Lee
Author: Dhilon S. Patel
Author: Siewert J. Marrink
Author: Yifei Qi
Author: Syma Khalid ORCID iD
Author: Wonpil Im

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