Mycolic Acids

Groenewald, Wilma; Bulacu, Monica; Croft, Anna; Marrink, Siewert-Jan (2019): Molecular Dynamics of Mycolic Acid Monolayers. ChemRxiv. Preprint.

Mycobacterium tuberculosis, the organism responsible for TB infection in
humans, is inherently resilient against host defences and anti-TB drugs. This
persistence is attributed partly to the presence of lipids, such as mycolic acids
(MAs), which make the cell wall impermeable. To study the conformational
dynamics of MAs, we present a coarse-grained model for a representative α-MA
(AMA) from Mycobacterium tuberculosis using the MARTINI force field. The
model is used to simulate monolayers of different sizes; a small monolayer
consisting of 220 MAs and a large monolayer consisting of 1972 MAs. The
model could replicate key features of experimental monolayers such as phase
changes and the collapse point. By studying the conformation of MAs in the
simulated monolayers, it was found that AMA did not fold into the W-
conformation at large surface areas but was only folded at the head group to give
a wide U-shape. On monolayer compression, the MA chains came closer
together, into a narrower U-shape, and an ordered monolayer was formed before
it collapsed.

The zip files below contain all the files needed to run the small and large bilayer systems using GROMACS.