Coarse-Grained Molecular Dynamics Simulation of Methane Interacting with Intracytoplasmic Membranes

Abstract

Intracytoplasmic membranes (ICMs) are a common structural element found in almost all methanotrophic bacteria. They house the particulate methane monooxygenase (pMMO), which is the initial enzyme in the metabolism of methane. To study the interaction of methane with these membranes we present coarse-grained molecular dynamics simulations using MARTINI force fields in the GROMACS molecular dynamics software package. All model lipid membrane were composed of a mixture of DOPG and DOPE. In some cases model hopanoids were added to the membrane. The study has three main considerations. First, in single membranes, both the partitioning of methane to the membrane and its effect on the fluidity of the bilayer was evaluated. Second, stacked membranes were created to model intracytoplasmic membrane layers and analyze the permeability of methane between these layers. Third, increasing amounts of model hopanoids were used to evaluate their effect on methane permeability and lipid mobility in the membranes.