The Outer Membranes of Gram-negative bacteria are asymmetric lipid bilayers, composed by standard lipids in the inner leaflet and mostly lipopolysaccharides (LPSs) in their outer leaflet. Outer membranes and their components are of critical importance for bacterial cell structure and function, as outer membrane proteins can regulate a diverse range of functions, while the organization and dynamics of LPSs can influence bacterial resistance against antimicrobial agents and cause toxic reactions in human hosts, leading to a number of diseases.
Despite their significance, the experimental study of outer membranes is challenging. Molecular Dynamics (MD) simulations can be a useful tool in modeling the structure and dynamics of membranes and membrane proteins. However, the preparation and simulation of outer membrane proteins in their native LPS-containing outer membrane environment is not straightforward.
The Gram-Negative Outer Membrane Modeler (GNOMM) is an automated workflow for the construction of LPS-rich outer membrane systems in MD simulations. GNOMM currently supports four widely used force fields, namely, the CHARMM36 all-atom, GROMOS 54A7 united-atom, MARTINI coarse-grained and PACE hybrid resolution models, and enables the building of membrane and protein-membrane systems with complex lipid bilayers containing LPSs. The generated output configurations can be subsequently used to perform Molecular Dynamics simulations with the freely available, high performance GROMACS simulation engine.
IMPORTANT! Read this announcement regarding the use of the GROMOS force field with GROMACS
Fotis A. Baltoumas, Stavros J. Hamodrakas & Vassiliki A. Iconomidou (2019)
The Gram-Negative Outer Membrane Modeler: automated building of lipopolysaccharide-rich bacterial outer membranes in four force fields
J. Comput. Chem. Jul 5; 40(18): 1727-1734, DOI: 10.1002/jcc.25823