CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides
Pin-Chia Hsu
School of Chemistry, University of Southampton, Southampton, SO17 1BJ United Kingdom
These authors contributed equally to this work
Search for more papers by this authorBart M. H. Bruininks
Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, Groningen, AG, 9747 The Netherlands
These authors contributed equally to this work
Search for more papers by this authorDamien Jefferies
School of Chemistry, University of Southampton, Southampton, SO17 1BJ United Kingdom
These authors contributed equally to this work
Search for more papers by this authorPaulo Cesar Telles de Souza
Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, Groningen, AG, 9747 The Netherlands
These authors contributed equally to this work
Search for more papers by this authorJumin Lee
Departments of Biological Sciences and Bioengineering, Lehigh University, Pennsylvania
These authors contributed equally to this work
Search for more papers by this authorDhilon S. Patel
Departments of Biological Sciences and Bioengineering, Lehigh University, Pennsylvania
Search for more papers by this authorSiewert J. Marrink
Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, Groningen, AG, 9747 The Netherlands
Search for more papers by this authorCorresponding Author
Yifei Qi
College of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062 China
E-mail: [email protected], E-mail: [email protected], E-mail: [email protected]Search for more papers by this authorCorresponding Author
Syma Khalid
School of Chemistry, University of Southampton, Southampton, SO17 1BJ United Kingdom
E-mail: [email protected], E-mail: [email protected], E-mail: [email protected]Search for more papers by this authorCorresponding Author
Wonpil Im
Departments of Biological Sciences and Bioengineering, Lehigh University, Pennsylvania
E-mail: [email protected], E-mail: [email protected], E-mail: [email protected]Search for more papers by this authorPin-Chia Hsu
School of Chemistry, University of Southampton, Southampton, SO17 1BJ United Kingdom
These authors contributed equally to this work
Search for more papers by this authorBart M. H. Bruininks
Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, Groningen, AG, 9747 The Netherlands
These authors contributed equally to this work
Search for more papers by this authorDamien Jefferies
School of Chemistry, University of Southampton, Southampton, SO17 1BJ United Kingdom
These authors contributed equally to this work
Search for more papers by this authorPaulo Cesar Telles de Souza
Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, Groningen, AG, 9747 The Netherlands
These authors contributed equally to this work
Search for more papers by this authorJumin Lee
Departments of Biological Sciences and Bioengineering, Lehigh University, Pennsylvania
These authors contributed equally to this work
Search for more papers by this authorDhilon S. Patel
Departments of Biological Sciences and Bioengineering, Lehigh University, Pennsylvania
Search for more papers by this authorSiewert J. Marrink
Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, Groningen, AG, 9747 The Netherlands
Search for more papers by this authorCorresponding Author
Yifei Qi
College of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062 China
E-mail: [email protected], E-mail: [email protected], E-mail: [email protected]Search for more papers by this authorCorresponding Author
Syma Khalid
School of Chemistry, University of Southampton, Southampton, SO17 1BJ United Kingdom
E-mail: [email protected], E-mail: [email protected], E-mail: [email protected]Search for more papers by this authorCorresponding Author
Wonpil Im
Departments of Biological Sciences and Bioengineering, Lehigh University, Pennsylvania
E-mail: [email protected], E-mail: [email protected], E-mail: [email protected]Search for more papers by this authorAbstract
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. © 2017 Wiley Periodicals, Inc.
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